Maintenance dialysis is a costly and resource intense activity. In Australia, inadequate health infrastructure and poor access to technically skilled staff can limit service provision in remote areas where many Aboriginal dialysis patients live. With most studies based on urban service provision, there is little evidence to guide service development. However permanent relocation to an urban area for treatment can have significant social and financial impacts that are poorly quantified. This study is part of a broader project to quantify the costs and benefits of dialysis service models in urban and remote locations in Australia’s Northern Territory (NT).We undertook a micro-costing analysis of dialysis service delivery costs in urban, rural and remote areas in the NT from the payer perspective. Recurrent maintenance costs  as well as capital costs were included. Missing and centralised costs were standardised; results were inflated to 2017 values and reported in Australian dollars.There was little difference between the average annual cost for urban and rural services with respective median costs of $85,919 versus $84,629. However remote service costs were higher , driven by higher staff costs. The inclusion of capital costs did not add substantially to annual costs. Annual home haemodialysis costs  were similar to other jurisdictions despite the significant differences in program delivery and payment of expenses not traditionally borne by governments. Annual peritoneal dialysis costs  were both higher than home and in-centre haemodialysis by recent national dialysis cost studies.The cost drivers for staffed services were staffing models and patient attendance rates. Staff salaries and transport costs were significantly higher in remote models of care. Opportunities to reduce expenditure exist by encouraging community supported services and employing local staff. Despite the delivery challenges of home haemodialysis including high patient attrition, the program still provides a cost benefit compared to urban staffed services. The next component of this study will examine patient health service utilisation and costs by model of care to provide a more comprehensive analysis of the overall cost of providing services in each location.The online version of this article (10.1186/s12882-019-1421-z) contains supplementary material, which is available to authorized users. Kidney disease is a significant health issue globally and disproportionately impacts disadvantaged populations –3. In AuAustralia has a publicly funded health care system predominantly based on the delivery and re-imbursement of defined activities . The AusThe NT has a relatively small population  sparsely dispersed over a large geographical are (1.3million square kilometres) . DialysiThe lack of staffed dialysis services in remote communities limits the opportunities for a patient to have treatment at home to self-care haemodialysis (HD), peritoneal dialysis (PD) and transplantation. However, transplantation rates amongst Aboriginal people are low, and PD and home HD make up less than 10% of all people requiring treatment. The demand for staffed services in the NT is therefore high at 75% of all kidney treatments. This is consistent with studies of First Nation people in Canada and New Zealand , but is Dialysis is a long-term treatment that can extend into decades. In the NT, as most staffed services are centralised in urban areas, permanent relocation for medical treatment and the subsequent dislocation, can have significant consequences for the individual as well as for government services. This is particularly stressful for Aboriginal people who are more likely to be affected at a younger age and when they are at their most active in their working and family life . The proIn response to escalating demand for dialysis treatments from the early 1990s, the NT government implemented measures aimed at quickly increasing capacity while containing costs. This perpetuated a model of large, centralised, urban services . While sThis study forms part of a broader mixed methods project using linked administrative data to examine the costs and benefits of various models of dialysis care in the NT and more widely in Australia . The finThis analysis focusses on dialysis service delivery costs from the payer perspective (DoH and PH). At the time of this study the partnership between the NT Department of Health (DoH) and Purple House (PH) consisted of the DoH providing PH a fixed annual amount and in-kind contribution for each dialysis treatment, equivalent to medical supervision, consumables and maintenance support available to a self-care patient. This was in line with the DoH policy of supporting services closer to home through self-care. PH covered all other expenditure for service delivery  . The cosAt the time of the analysis, the NT was caring for more than 725 patients with end stage kidney disease. The mean age of patients was 45 years with a slightly higher proportion of females to males. A small proportion of patients were undertaking self-care HD and PD (less than 10%) and approximately 13% were living with a transplant . Most paRenal services in the NT are organised on a notional “hub and spoke” model, where the “hub” or tertiary provider oversees service delivery by other dialysis services. In the NT, larger urban staffed facilities function as hub services. We examined expenditure by location and service type, allocating the service to one of five dialysis models of care (DxMoC) described in detail in Table This study uses geographic descriptors for dialysis locations consistent with local views and vernacular e.g. “urban”, “rural” and “remote”. Australia uses a nation-wide framework to systematically classify the relationship between geography, population and services access . HoweverFinancial data from the DoH included expenditure reports for all renal related cost centres and Service Level Agreements with PH for 2013/14. Direct and overhead expenditure incurred by the DoH on behalf of PH  were calculated and added to the cost model. Pharmacy costs were based on the cost calculation for DxMoC1, as patients rotated through both services. PH also provided Profit and Loss statements for 2016/17 allowing independent analysis of the income and expenditure attributed to dialysis services . All costs have been reported in 2017 Australian dollars.Capital costs for each service were based on original construction costs or recent construction costs of facilities of similar size and location. Equivalent annual costs were calculated for capital costs based on the working life of the capital (provided by DoH) of 40 years or less, assuming no resale value and a 5% discount rate .Direct and Shared resources. Within the Direct cost of service provision, expenditure was separated into Salary, Variable Costs and Fixed Costs. Allocation of Shared costs e.g. medical, allied health and educator staff working across a number of sites or models of care, were calculated for each model according to time allocations as advised by the relevant staff. Other overhead costs (e.g. corporate services) were based on nationally derived values [We used a micro-costing approach and analysed service costs for d values . One-offAs the data were from different time periods and sources, to enhance comparability across models of care, we assumed consistent values for some items based on available and representative data provided by DoH. This included year 2017 processing costs , service floor plans and facility life spans based on construction materials and locations.The Australian Government subsidises the cost of most medications for all residents through the Pharmaceutical Benefits Scheme . Those wMedication costs were estimated from 12 months of dispensed scripts; unit costs were from the Pharmaceutical Benefits Scheme Dispensed Price for Maximum Quantity (DPMQ) costs . ErythroPathology costs were based on the total type and number of blood samples taken in a year and calculated on Medicare Benefits Schedule (MBS) fees for service items .The availability of staff accommodation in rural and remote sites is critical to service sustainability. Accommodation is often subsidised  or provided (remote) but entitlements were not offered consistently in our study by service providers, making comparisons difficult. The cost of providing staff accommodation were not included in the cost study.Costs were adjusted to a base year of 2017 Australian dollars using the Australian Institute of Health and Welfare (AIHW) Health Price Index  unless oprescribed dialysis treatments more or less than three times per week. PD costs were calculated per patient per year.The aim of the micro-costing approach was to identify the average cost per treatment (CPT) for each model of care identified in Table Overall, and after adjustments, we found that the annual costs of service delivery in urban and rural areas were similar but remote based services were significantly higher. The co-location of facilities with other health services conferred some cost benefits through shared infrastructure and systems including storage, supply lines and facility management. The rural and remote models were more likely to sustain higher nursing costs related to staff entitlements for remoteness and recruitment, relocation and agency fees. Costs for visiting staff from the hub services had relatively small impacts.Variation within models related to different staffing ratios, waste management practices  and staff and patient transport costs. Salaries made up more than 50% of total costs and were also the main driver for cost differences between staffed models followed by capital depreciation. All models were particularly sensitive to low volume services.Four urban services (DxMoC1), two based in the Top End and two in Central Australia, treated the majority of NT dialysis patients. Only one DxMoC1 in each region acted as a hub service. In the Top End, the hub service oversaw the management of a smaller urban facility that sat within a larger health complex 30 km away. Staff were rostered from the hub service and often allocated on an ad hoc basis to the smaller facility. Consumables also flowed through the hub service.In Central Australia, the hub service was co-located with other health services in a single health complex with some expenditure allocated on a cost sharing basis. This model included costs not evident at other services such as security and vehicles for patient transport. A second DxMoC1 facility was contracted as a public/private partnership. This facility delivered dialysis services for the NT government on a ‘price per treatment’ (PPT) basis where the PPT covered infrastructure, salaries and operational costs of the service. Payment was based on completed treatments irrespective of total patient numbers or staffing levels at the facility. Some services provided by the DoH (e.g. pharmacy items) but reimbursed by the contractor could not be captured as funds were absorbed into general revenue. Therefore, it is likely costs for this service were slightly overestimated. Medical staff, Allied Health, and non-dialysis pharmacy costs not included in the PPT were calculated as per other models. Depreciation was not calculated for this model, and line item comparisons could not be undertaken as these costs were included in the PPT. These costs have been represented as variable costs as they fluctuated according to the number of treatments completed.Infrastructure costs for DxMoC1 were based on recent construction costs and calculated according to the size of the facility. Depreciation was annuitised over 40 years using a discount rate of 5%.Average annual cost per patient varied from $80,566 to $91,101 for DxMoC1 with a median per patient per year cost of $85,919. The Top End hub service had the highest annual per patient cost at $91,918 while the Central Australia contracted service (public/private partnership) had the lowest annual cost at $80,566  were co-located with local hospitals in an attempt to ameliorate these factors. At the time, they were one third the size of their urban counterparts. These smaller services tended to operate with lower ancillary staff, such as patient care assistants, administration staff and nurse managers. While staff costs were the main cost driver, the Central Australia DxMoC2 experienced higher costs related to recruitment, relocation and remote area allowances equating to a 13% difference in the overall salary costs. Annuitisation of capital costs, based on recent facility construction costs, assumed a 30 years working life and a 5% discount rate. The average annual cost per patient was $81,009 for the Top End and $88,249 for Central Australia with a median annual cost of $84,629 for DxMoC2  in the NT commenced in 1998 with the establishment of a six-station facility on an island 80 miles off the coast of the NT. The stand-alone facility is independent of other health services on the island and remains the only remote service fully managed by the government in the NT. Care was overseen by the Top End hub service (DxMoC1) and renal nursing and ancillary staff rotated via air from the mainland on a weekly or more frequent basis. A weekly barge service provided transport to and from the island for equipment, consumables and waste. Some administrative activities , borne by the DxMoC1 hub service, were difficult to track and therefore it is likely that the full costs of service delivery for this model were under-estimated.At the time of the study, the PH provided dialysis services in several remote areas (DxMoC4) in partnership with the DoH. As noted, services were not contracted by the DoH but they provided funding support in a small annual grant and ‘in-kind’ contribution for each treatment delivered, equivalent to the consumables provided to self-care patients. PH is overseen by a Board of lay Directors made up of Traditional Land Owners and Elders. The service is staffed by a multidisciplinary team of paid professionals and volunteers. All dialysis is provided by trained nursing staff and the organisation is accredited with the required Australian Health Care bodies.Historically the model was one of respite. Select relocated patients attending the urban government service (DxMoC1), were offered short periods of staffed dialysis care at home (DxMoC4). However, the success of PH in sourcing alternative government and philanthropic funds, as well as greater support from Traditional Land Owners, saw expansion of DxMoC4 sites across the NT. PH also operates on a hub and spoke model with the urban base in Central Australia managing remote service delivery.While both DxMoC3 and DxMoC4 were delivered in remote and very remote areas, DxMoC3 was a single stand-alone facility, whereas DxMoC4 delivered services in smaller facilities over many sites, including the border communities of Western Australia. Costs were based on the aggregated data of eight sites for DxMoC4.Driven predominantly by staff costs, annual costs per patient for both services were high compared to DxMoC1 and DxMoC2. Staff in remote areas attract higher salaries and allowances compared to similar positions in urban areas due to the requirement to operate independently. Salaries made up 57% of overall costs but staff travel costs were significantly higher at DxMoC3, driven by the staffing model which involved weekly or more frequent rotations from the urban service. In contrast DxMoC4 staff stayed in the community for weeks to months at a time.However, variable costs for DxMoC4 were more due to the consumable cost differences for the dialysis treatments. As DxMoC4 delivered the majority of their services from low volume two station facilities, treatment costs, which included dialysis machinery and maintenance, were treated the same as home HD, which was charged at a higher rate.Annuitisation of capital costs assumed a life span of 30 years for DxMoC3, a brick and mortar facility, while DxMoC4 capital costs were calculated on eight relocatable facilities with a life span of 25 years. Despite the different infrastructures, the annual equivalent costs for the DxMoC4 aggregated sites were similar to DxMoC3, which was sensitive to treatment volume.Overall Fig. , there wSelf-care therapies are generally considered the preferred treatment option from a financial and quality of life perspective, although they are also noted to be potentially more burdensome for some patients and carers –38. In tThere were significant differences in the delivery of the home therapies program in the NT compared to other jurisdictions. Most patients were Aboriginal and returned to the remote area once trained. Training periods tended to be longer due to language differences, lower literacy and numeracy levels, unfamiliarity with technology and inconsistent attendance. Frequent home visits to patients were a key feature and therefore staff ratios were higher. Self-care HD also included infrastructure costs. The specifically designed ‘two station’ treatment facilities were provided by the government in recognition of the poor state of many homes in remote communities.The average self-care HD training time was 6.1 months (2 to 12 months) for Aboriginal people and 4.8 months (3 to 7 months) for non-Aboriginal people, with approximately 30% of both groups withdrawing from the program after 2.8 months. Staff to patient ratios for self-care HD training were 1.43 staff for four patients in training. Staff travel costs were comparatively high for both the training component (exploratory and consultative remote site visits), and when patients were established at home (to check conditions and techniques). Fixed costs associated with the management of the dedicated HD infrastructure included leasing fees, rates and cleaning; costs generally not incurred in other jurisdictions.Equivalent annual costs were estimated for capital costs for both the training facility and remote sites (assuming a 25 years working life) and calculated on a cost per treatment basis. Remote sites assumed four patients in attendance. Average annual costs per patient for home HD were $66,639 in the first year and $42,927 in the second and subsequent years  which was one third more expensive than continuous ambulatory peritoneal dialysis (CAPD). Capital costs were only allocated for the training component.The average annual per patient cost in the first year were $87,250 with costs in the second and subsequent years at $58,489  compared to rural and remote services (over 90%). Our experience suggests that patients who are forced to relocate to access urban services have poorer attendance.The PP (contracted) DxMoC1 service in Central Australia was the least expensive of all the urban and rural staffed facilities. The PP service routinely achieved nearly 100% attendance. In part this was due to the contract conditions specifying reimbursement according to attendance. This in turn, motivated management and staff to support patients to attend. Additionally, the contracted service had limited responsibilities for broader renal program delivery compared to the hub service.An expectation that services in rural and remote locations cost considerably more proved only partially true. The cost drivers for these locations related to staffing models and subsequent salary and travel costs. Services that employed local staff (DxMoC2) had similar overall costs to urban services, while services that employed a fly-in fly-out model (DxMoC3), spent considerably more on salaries, allowances and staff transport.less expensive than the cost of delivering care at a single remote site (DxMoC3). During the period of analysis, DxMoC3 and the multiple locations of DxMoC4 were never at capacity and patient numbers fluctuated over the year. However, adherence to the prescribed number of treatments for individuals attending remote services  was better than the urban services, averaging over 90%. We surmised that these services, perhaps by virtue of their smaller size and proximity to community and family, facilitated closer relationships and provided opportunities for more personalised care, resulting in better attendance.The DxMoC4 community-controlled service was generally perceived as a high cost model of care, primarily because services were delivered from multiple, small, low volume sites and because the model offered a comprehensive program of social and cultural support, unlike the other models. Despite this and the higher per treatment costs, our analysis found the service was The first year costs for both self-care therapies (HD and PD) were higher than in other cost studies , primarily due to more lengthy training programs and associated staff costs , 42, 43.Our study found the PD program was considerably more expensive than the home HD program, driven by the much higher PD consumable costs, despite the additional machinery and maintenance costs of HD. PD costs mirrored early cost studies in Australia  but not To our knowledge this is the first comprehensive exploration of dialysis services costs in remote locations in Australia. The study took a micro-costing, top down approach and applied a rigorous methodology in the analysis of the data. We used the best available data from multiple sources and went to significant lengths to locate missing information.However, we acknowledge that our analysis also has some limitations. We have focussed on recurrent costs of each ‘outpatient’ service for maintenance dialysis and did not include in-patient or in-centre dialysis related costs. There were challenges with incomplete data and separation of costs where service costs were centralised, single cost centres for different types of activities existed and supply lines or facilities were shared. Assumptions and calculations were based on advice from corporate, financial and clinical staff working in these areas.Given the demand for services closer to home, where “home” is in a remote location, our study identifies opportunities for cost minimisation of dialysis services. Models of care embedded within communities, employing local staff, achieve cost efficiencies by reducing personnel and travel costs. With high levels of unemployment in remote communities in the NT  there aOur cost study provides the basis for the next component of this research which evaluates the broader health service utilisation costs , associated with a patient’s preference for a model of care. The relationship between health service uptake, facility size and location will be explored as will the costs of transitioning between models of care, particularly for the self-care therapies. The addition of these annual hospital costs to the model of care they attend, will provide a more accurate reflection of service delivery costs per patient per location and model of care.Additional file 1:Geographic classification of study sites compared to local terminology. Comparison of study location designations and the official Australian classifications for remoteness. (DOCX 13 kb)Additional file 2:“What is the Purple House?”. Description of data: Additional information on development and role of Purple House. (DOCX 2872 kb)


Despite their ubiquity in Holocene African archaeological assemblages, ostrich eggshell (OES) beads are rarely studied in detail. An exception is in southern Africa, where there is a proposed relationship between OES bead diameter and the arrival of herding ~2000 years before present. In 1987, Leon Jacobson first observed that beads from forager sites in Namibia tended to be smaller than those associated with herder sites. Studies examining bead size around the Western Cape have generally confirmed Jacobson’s findings, though the driving forces of the diameter change remain unknown. Since this time, diameter has become an informal way of distinguishing forager and herder assemblages in southern Africa, but no large-scale studies of OES bead variation have been undertaken. Here we present an expanded analysis of Holocene OES bead diameters from southern, and for the first time, eastern Africa. Results reveal distinct patterns in OES bead size over time, reflecting different local dynamics associated with the spread of herding. In southern Africa, OES diameters display low variability and smaller absolute size through time. While larger beads begin to appear <2000 years ago, most beads in our study remained smaller. In contrast, eastern African OES bead diameters are consistently larger over the last 10,000 years and show no appreciable size change with the introduction of herding. Notably, larger beads thought to be associated with herders in southern Africa fall within the range of eastern African beads, indicating a potential connection between these regions in the Late Holocene consistent with genetic findings. Regional differences in bead size are subtle, on the order of millimeters, yet offer a potentially important line of evidence for investigating the spread of herding in sub-Saharan Africa. In order to understand the meaning of these changes, we encourage additional studies of OES bead assemblages and urge researchers to report individual bead diameters, rather than averages by level. Ostrich eggshell (OES) beads are among the oldest known ornaments made by our species and are often found in archaeological assemblages throughout Africa –4. AlthoThirty years ago, Leon Jacobson ,6 proposHere we present an expanded analysis of OES bead diameters from across the Holocene of southern and eastern Africa to explore their diversity on a greater scale. This allows us, for the first time, to test the hypothesis that larger bead diameters are associated with the appearance of herders in two separate geographical areas. We re-evaluate previously published bead diameters from nineteen sites and add datasets from eleven additional sites in Botswana, Kenya, Tanzania, Namibia, and South Africa. By using individual bead diameters rather than averages by level, we increase the dataset on Holocene OES beads from less than 100 data points to >1000. This permits a considerably more nuanced exploration of cultural behaviour as reflected in beads. We recommend future studies adopt this approach in order capture subtle variability within levels and time periods that is masked when bead averages are reported by level.Beads are often overlooked as analytical units, yet their roles in social expression, identity signaling, and exchange may offer important insights into aspects of the past that are not apparent from other lines of evidence –18. BecaPastoralism, or herding domestic animals, was the first form of food production to spread across Africa . HerdingHerding entered eastern Africa through northwestern Kenya ~5000 BP as Lake Turkana receded, exposing new pasturelands –27. The Cattle did not spread further south for several hundred years, potentially limited by novel livestock disease vectors south of Lake Turkana ,32. By ~Domesticated caprines entered southern Africa ~2000 BP, although the route(s) and mechanism(s) of this process are contested ,38–42. AIn southern Africa, competing models for how herding spread must account for the rapid movement of sheep and their low proportions at sites that otherwise yield Later Stone Age (LSA) artifacts. Sheep/goats appeared on the western and southern coasts of South Africa ~2000 BP, virtually simultaneously with their arrival in Namibia ~2200 BP and northern Botswana ~2000 BP ,38,42,50Genetic evidence suggests migration and admixture were factors in the spread of herding to both eastern and southern Africa. Based on ancient DNA (aDNA) analysis of 41 foragers and early food producers from Kenya and Tanzania, Prendergast et al.  propose Some eastern Africans herders were seemingly involved in the transmission of herding father south. A ~1200-year-old individual from a herder context at Kasteelberg in South Africa exhibits ancestry related to both southern and eastern African populations, with 40% of her ancestry related to an infant from the PN herder site of Luxmanda in Tanzania . These fHerding’s spread into eastern and southern Africa followed different trajectories in terms of timing, pace, landscapes, and human populations involved. These differences are reflected in distinctive material cultural records, which may extend to differences in OES beads. And yet, these processes were part of a larger movement of non-African domesticates through sub-Saharan Africa. The introduction of sheep, goats, and cattle from the north involved, to varying extents, the same mechanisms of demic diffusion, local adoption, interaction, and innovation as economies shifted and herders and foragers established new relationships. Both regions were then further impacted by the later arrival of Bantu-speaking farmers. The persistence of foragers in both regions across these transitions suggests disparate groups were involved in complex interactions. With this in mind, personal ornaments such as OES beads may provide clues as to how goods and people moved through these landscapes and were influenced by the changes around them.OES beads are abundant at Holocene sites in eastern Africa but there has been little systematic study of bead size or attributes. A notable recent exception is Tryon et al. , where mConsiderably more attention has been paid to OES bead variation in Holocene southern Africa. Jacobson ,6 suggesBead diameter was soon adopted by researchers looking for ways to differentiate forager from herder archaeological assemblages and to distinguish herders from foragers on their periphery who may have used livestock as part of their seasonal cycle. By looking at bead size change through time at sites in the Western Cape, Smith et al.  observedSubsequent studies sought to test changes in bead diameter in other parts of southern Africa –13,70,71Despite an emerging picture of complexity across time and space, there has been limited consideration of results between studies. When these early bead data are plotted on a single graph, the inverse relationship between bead size and time is evident . HoweverWe measured, or compiled published measurements, for beads from Holocene deposits from eight sites in eastern and 22 sites in southern Africa n = 1200) , Table 1200 , TabPrevious work by Yates  advocateFor most of the new data, bead diameter was measured manually (by JM) using standard digital calipers. A few collections  were studied at the University of Alberta while exported on-loan by their respective excavators, while other collections  were studied in the southern African museums in which they are curated  typically reflect the average of measurements for multiple beads that can only be entered as a single point. All data used here are available in the This is not an exhaustive list of OES beads from eastern and southern African Holocene archaeological sites. We chose a subsection of sites with deposits spanning the spread of herding to these regions, and that had beads with published data or those that were accessible for study, with known provenience and associated radiocarbon dates. We hope that this model will be expanded in the future to incorporate additional datasets.For this study we use the terms ‘larger’ and ‘smaller’ only as relative descriptors within these datasets, and not to refer to absolute size cutoffs. There have been varying definitions of ‘large’ and ‘small’ beads in the literature in the context of their relationships to hunters and herders. Jacobson’s ,6 data iGraphing the new individual bead diameters in addition to the previously published measurements provides a more nuanced perspective of the southern African data . There iLarger beads do not appear in greater numbers until <2000 BP. In fact, all recorded beads older than 2500 BP (n = 506) are 6 mm or smaller, with only three exceptions . The direct date on the Dunefield Midden bead renders its age reliable, however the other two cases should be regarded cautiously for several reasons. The Nelson Bay Cave assemblage was excavated from 1964–1979 and went through changes in layer naming systems as well as a transition from imperial to metric measurements. Wonderwork Cave has been excavated intermittently since the 1940s and also went through several layer naming conventions, summarized in . It is tA different pattern emerges for eastern Africa. Compared to southern African diameters, bead sizes in eastern Africa are greater over the last 10,000 years, and do not appear to change after the introduction of herding. Average bead diameter from assemblages >4000 BP is 6.15 mm, with a range of 4.39–9.15 mm (n = 188). Beads younger than 4000 BP have a mean of 6.65 mm with a range of 4.73–14.49 mm (n = 112). The 14.49 mm specimen is an unusually large outlier, and the next largest beads are <10 mm. Although diameter changes slightly through time, overall bead size remains variable.Comparing eastern and southern African datasets reveals different regional patterns . The easPatterns of OES bead diameter in eastern and southern Africa are patently different. Both regions acquired herding through contact with populations from the north, and both regions had prior, long-standing OES bead traditions. Yet regional and temporal patterns in OES bead diameters reflect this transition in unique ways. This begs the question of what beads can tell us about the introduction of herding to different parts of the continent.In eastern Africa, OES beads size did not appear to change with the arrival of herding despite other shifts in material culture. This may be, at least partly, because livestock were adopted by local foragers who retained their bead-making traditions. It is also possible that migrants entering eastern Africa possessed similar bead traditions, or adopted local traditions soon after arriving through contact and/or integration with foragers. These possibilities are not mutually exclusive, and multiple factors likely contributed to herding’s spread. However, using beads to distinguish between different trajectories requires further research on pastoralist artifact assemblages farther north. OES beads have been reported from numerous sites in the Nile Valley including Gebel Ramlah , el BargIn eastern African sites where beads are known from both pre- and post-herding contexts, there is virtually no change in bead diameter over time. Although it is unclear for many of the measured sites whether beads were associated with herders or foragers, after ~3000 BP these groups were likely in contact, or at least aware of one another. If the development of PN traditions in the Rift Valley disrupted pre-existing social networks, this is not reflected in OES bead diameters.In southern Africa, there is a detectable change in bead diameters that appears to correlate with herding’s spread. Although the exact timing is disputed, zooarchaeological data support an initial entrance of sheep/goats around 2000 BP, exactly when a subset of >6.5 mm OES beads appear. The introduction of new bead sizes seems coeval with the arrival of herding, but larger beads did not replace existing traditions or become dominant in the assemblages we sampled. This is consistent with other evidence of cultural continuity in the archaeological record ,40. Two These results also lend support for Jacobson’s ,6 originComparisons of eastern and southern African OES bead assemblages support other lines of evidence showing different trajectories in the introduction of livestock and herding. Although both scenarios likely involved population interaction and exchange, there is only an observable change in bead styles in southern Africa. Examining these different patterns more closely in conjunction with other archaeological data may reveal what interactions looked like and unique pathways to food production on the African continent. Since OES beads were used by foragers for more than 40,000 years in both regions, change—or lack thereof—in bead styles is informative about how foragers responded, coped, and mediated cultural contact and economic change. Given the ubiquity of OES beads at African archaeological sites bridging this transition, beads constitute important evidence for how the arrival of herding impacted diverse human landscapes.Patterns in OES beads may also provide an independent line of evidence connecting eastern and southern Africa in the Late Holocene. The hypothesis that sheep and goats were introduced to southern Africa by migrants who were the ancestors of Khoekhoen herders, has a long history of debate in southern African archaeology . Multiple genetic studies now document gene flow from eastern to southern Africa around the time herding spread, providing unequivocal evidence of contact between these regions consistent with other lines of archaeological evidence. This is especially evident in the shared ancestry of girls buried at Luxmanda, Tanzania and Kasteelberg, South Africa . What rePatterns in southern African OES beads seem to parallel genetic evidence for interregional contact, but add the perspective of cultural identity rather than genetic ancestry. OES beads similar in diameter to those from eastern Africa appeared around the same time as livestock, but did not replace existing smaller bead traditions. One explanation for this is that small numbers of migrant herders brought finished beads and/or produced beads using eastern African stylistic norms. These items then entered local knowledge and exchange networks along with livestock and herding practices. It is also noteworthy that both genetic and bead evidence suggests this was a unidirectional process—neither smaller beads, nor southern African genetic signatures, appear to flow back to eastern Africa. Whether beads capture an additional link between eastern and southern African populations around 2000 BP is an intriguing possibility that should be tested through future research.A final point that emerges from this research is the importance of reporting individual bead diameters instead of a single averaged calculation by excavation or stratigraphic level. Comparing Figs Beads constitute a crucial component of African archaeological assemblages, but their usefulness for exploring transitions in the past has been largely overlooked. Reassessment of published and new data on bead size diameter supports Jacobson’s ,6 observThese findings should now be evaluated against other lines of archaeological evidence and tested with additional datasets from these regions and other parts of the continent. Future research should also investigate related questions on bead origins, manufacture, and use, e.g., the effects of taphonomic processes and wear on bead diameter ,96, regiS1 File(PDF)Click here for additional data file.S1 TableEntries 1–44 are published diameters, 45–1220 are new data. For new data, reference refers to publication of the ages. All Kisese II diameters were measured by Dr. Christian Tryon. Wherever possible, published radiocarbon ages were calibrated using the Intcal13 dataset  and grap(XLSX)Click here for additional data file.S1 References(DOCX)Click here for additional data file.


Pestivirus, which belongs to the family Flaviviridae, includes ssRNA+ viruses responsible for infectious diseases in swine, cattle, sheep, goats, and other domestic and wild animals. Recently, several putative pestiviruses species have been discovered and characterized in mammalian species ; one of these is a genetically distinct pestivirus, named atypical porcine pestivirus (APPV), discovered using the next-generation sequencing technology. APPV has been detected in piglets with congenital tremor (CT) from four different continents, including North America, South America, Europe, and Asia. There is strong evidence that experimental inoculation and in field outbreaks involving APPV induce CT in piglets. Additionally, splay leg (SL) syndrome has been observed concurrently with CT, and it was induced by APPV in experimental studies and some field cases. Animals with a persistent and/or chronic infection condition can shed the virus over time. Viral-RNA is frequently detected in different tissues from CT-piglets; however, high loads of APPV are detected most consistently in central nervous tissue. Moreover, the APPV genome has been recently detected in semen and preputial swabs from boar studs, as well as in serum and tissue samples from wild boars and domestic adult pigs, all known to be clinically healthy. Phylogenetic analysis revealed that the APPV sequence  exhibits high genetic diversity between viral strains detected in different countries and formed independent clusters according to geographic location. Additional studies are needed to evaluate the molecular detection and sero-prevalence of APPV around the world. Lastly, more research is needed to understand clinical presentations associated with APPV infection, as well as the economic losses related to the virus in pig production worldwide.The genus  Piglet pre-weaning mortality is a major problem in pig farms around the world. On average, pre-weaning mortality rates of live-born piglets can be as high as 23% and starvation and crushing are the main causes of death . DiffereHistorically, CT was first reported in the literature 97 years ago, when Kinsley  describePestivirus with the occurrence of CT in newborn piglets. It was usually described as a temporary condition, lasting several weeks to months, and characterized by tremors of the head, limbs, and body, varying in severity and intensity. However, the clinical signs were reduced or absent during inactivity or sleep  was first identified in 2015 , severalor sleep , 10.In general, CT is not the cause of death in affected piglets; however, their survival may be threatened because of inadequate colostrum, or milk intake, leading to severe growth retardation and death by starvation or crushing due to impairment of evasive actions , 7. FurtAlthough the impact of most exotic diseases in animal production and global economy is known , a more Pestivirus, which belongs to the family Flaviviridae (ssRNA +), includes 11 recognized species: Pestivirus A , Pestivirus B , Pestivirus C , and Pestivirus D (border disease virus), Pestivirus E (pronghorn pestivirus), Pestivirus F (Bungowannah virus), Pestivirus G (giraffe pestivirus), Pestivirus H (Hobi-like pestivirus), Pestivirus I (Aydin-like pestivirus), Pestivirus J (rat pestivirus), and Pestivirus K   .Additionally, three atypical pestiviruses have been characterized in pigs: Bungowannah virus (causing myocarditis), APPV and Linda virus  , 13, 14.Pestivirus and its high genetic diversity constitute a worldwide concern.Further characterization of APPV, as well as other porcine pestiviruses linked to severe clinical diseases in pigs, is needed , 19. RemAPPV has been detected in four different continents, including North America, South America, Europe, and Asia, and in countries such as the United States (first report) , 10, theAPPV-associated CT has been reported to be more prevalent in litters of gilts than sows , 4, suggAdult domestic pigs , 16, 21 A retrospective analysis of cerebellum samples from Germany and another retrospective study with fresh and formaldehyde-fixed paraffin-embedded tissue samples from Hungary showed the presence of APPV in CT-affected piglets from over a decade ago , 27. SimWild boar is also susceptible to APPV infection, although its role in the virus epidemiology is unknown . LimitedRegarding to diagnosis, Postel et al.  describeThe newly discovered APPV  is capabAPPV has a wide distribution in tissue samples, excretion and secretion fluids , 22, 32.The economic relevance of an APPV-outbreak loss in pig production worldwide remains undetermined; however, it is estimated that the number of weaned piglets per sow decreases by > 10%, affecting reproductive performance. Additionally, mortality increased up to 30%, when CT-affected new-born piglets died of malnutrition in a farm in Austria  reportedIn China, Shen et al.  reportedThe impact of APPV infection on pig production seems to be indirect, since the mortality of CT piglets is the only loss reported so far, and it is mainly attributed to secondary factors. So, further studies evaluating its impact on pig production should be performed in order to estimate the direct loss in affected piglets, or suggest that the indirect loss could be related to the depletion of the immune system, such as what is reported in other pestiviruses.Pestivirus K species is ~10.8–11.5 kb. The APPV genome has ~25–28% pairwise identity to known pestiviruses and 68% pairwise identity to a recently partially characterized Rhinolophus affinis pestivirus, placing both viruses in a highly divergent lineage of pestiviruses  exhibit high genetic diversity between viral strains detected in different countries , 29–31 aA phylogenetic tree based on Bayesian analysis of 20 complete APPV polyprotein sequences and other pestiviruses demonstrated a monophyletic cluster topology for APPV. In addition, five distinct clusters were observed within the APPV clade  adaptive immunity of gilts/and sows; (2) possible transmission of the virus by semen; (3) absence of a commercial vaccine. For this reason, we hypothesize and suggest a few insights that may have a positive impact on the control of the infection. Since the highest prevalence of CT-piglets occurs in gilts, we suggest that the immune status of the dam and the time of infection are the key factors related to disease development. So, we recommend the use of an acclimatization strategy for replacement gilts, similarly to the protocol used for  protein , we stroFinally, even though the potential for intercontinental spread of some viruses and the impact of exotic and emerging diseases on worldwide pig production is known, we strongly recommend additional epidemiological studies that will provide current essential information regarding APPV and elucidate possible routes of entry, dissemination, and genetic evolution of APPV, as well as other viral agents. This data will aid in the active surveillance of pathogens considered exotic and/or emerging around the world .All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Cassava brown streak disease (CBSD) is a severe virus disease of cassava and prevalent in the eastern regions of Africa. The disease is characterized by distinct vein chlorosis and streak symptoms on leaves and stems and necrosis of storage roots. This necrosis can encompass large areas of the root, rendering it inedible so that the entire cassava harvest can be lost. African cassava varieties are susceptible to either of the two viruses causing the disease, cassava brown streak virus (CBSV) and Uganda cassava brown streak virus, and while there are less sensitive varieties, all cassava eventually succumb to the disease. The lack of CBSD resistance in African cassava varieties prompted this search for new sources of virus resistance in the diversity of South American cassava germplasm held in the collection at International Center for Tropical Agriculture, Columbia. Our search for CBSD resistance in South American cassava germplasm accessions revealed that most of the 238 South American cassava lines infected with CBSV established systemic virus infections with moderate to severe disease symptoms on leaves and stems. Fifteen cassava accessions did not become virus infected, remained free of symptoms, and CBSV was undetected by qRT-PCR. When tuberous roots of those lines were examined, necrotic tissue was found in eight lines and CBSV was detected. The remaining seven cassava accessions remained clear of symptoms on all tissues and organs and were virus free. A broad spectrum of virus resistance also including other virus isolates was confirmed for the breeding lines DSC167 and DSC118. While detailed infection experiments with other cassava lines selected for resistance are still ongoing, this indicates that the resistance identified may also hold against a broader diversity of CBSVs. Taken together, we present the results of a comprehensive study on CBSV resistance and susceptibility in cassava germplasm accessions from South America. The virus resistance in cassava germplasm identified provides compelling evidence for the invaluable contribution of germplasm collections to supply the genetic resources for the improvement of our crops. UCBSV and CBSV (U/CBSV) while genetically distinct, cause similar symptoms in leaves, stems, and root tissues of cassava (Cassava brown streak disease (CBSD), the most serious threat to cassava cultivation in East and Central Africa, is caused by two virus species, s UCBSV; , both me cassava , includi cassava . Despite cassava . The imp cassava  in the rin vitro collections at the International Center for Tropical Agriculture (CIAT), Cali, Colombia. Around 630 accessions of this collection represent its core diversity . The tissue cultured plants were propagated in vitro, hardened, and subsequently established in the glasshouse and grown under ambient conditions at 26 to 30°C with additional light provided.The South American cassava germplasm lines (238) were obtained as tissue cultured materials from the CIAT germplasm collectionFor all virus experiments, the CBSV reference isolates CBSV-Mo83 , CBSV-Ug65 (DSMZ PV-0996), and CBSV-Tan70  and the UCBSV reference isolate UCBSV-Ke125  were used. The viruses were maintained in the cassava varieties TME7 or TMS-96/0304 that were propagated through stem cuttings to produce sufficient amounts of axillary buds for grafting.Bud grafting similar to the method described by Prior to virus screening, the pathogenicity of virus isolates was assessed by comparing symptom severity and virus titer to then use the most aggressive virus isolate for a first, large-scale virus screening. For the bioassay, five plants of two African varieties – the variety “Albert,” which responds with severe symptoms to U/CBSV infections (sensitive), and the resistant variety “Namikonga,” responding to virus infections with limited symptom expression (tolerant)  – were iSymptoms on leaves were assessed using a severity scale ranging from 1, for leaves without symptoms, to 5, for severe symptoms on leaves . The meaFor large-scale virus screening, symptoms on cassava leaves and stems were evaluated using a severity record S that was defined for the purpose: S0, no symptoms on leaves and stems; S?, inconspicuous symptoms on leaves and stems; S+, moderate symptoms on leaves only; S++, severe symptoms on leaves and stems; and S+++, wilting of the stem followed by plant death.For the initial screening, the virus isolate CBSV-Mo83 was used to infect cassava. Plantlets established from tissue culture (two to three plants/accession) were infected by bud grafting, checked for the infection status at 10 dag, and inspected for symptom development. Cassava plants that remained symptomless for 1 month were decapitated by removing the apical parts of the shoots to force flushing of axillary buds. Viruses were monitored for a further 4 to 6 weeks. All cassava plants subjected to bud grafting, including those highly susceptible plants that wilted and died within the first 2 to 3 weeks after grafting, were tested for virus presence by qRT-PCR. Virus symptoms and detection of CBSV by qRT-PCR were taken as proof for susceptibility of a cassava accession, and even if only one plant became infected, the line was discarded and exempt from further testing. Monitoring and virus testing continued with symptomless and qRT-PCR-negative plants for a further 5–8 months, after which cassava lines that remained free of symptoms and virus were subjected to a second round of virus screening using five plants per cassava line .To study virus movement in the cassava accession DSC167 that was found highly resistant against CBSV, scions  from this line were side grafted  onto hea®fluorometer  using the Qubit RNA BR Assay Kit . Virus analysis by qRT-PCR was carried out by either an ep realplex4  Mastercycler equipped with the realplex4 software or a qTOWER3  equipped with the qPCRsoft evaluation software.RNA from cassava was extracted using an RNA extraction kit following the manufacturer’s protocol . The integrity of the RNA was analyzed by gel electrophoresis, and RNA was quantified in a QubitFor virus quantification in the varieties Albert and Namikonga, a SYBR Green qRT-PCR assay was performed using published primer sets  and cassOne microliter of total RNA (20 ng/μl) was converted into cDNA in a reaction mixture containing 5 μl of Moloney Murine Leukemia Virus Reverse Transcriptase (M-MLV RT) buffer (2×), 0.25 μl of dNTPs, 0.3 μM oligo(dt), 0.3 μM random hexamer primers, 0.2 μl of M-MLV RT, and nuclease-free sterile water to reach a reaction volume of 25 μl. cDNA synthesis was done for 30 min at 43°C and diluted fivefold prior to SYBR Green Kapa  qPCR. Reaction mixtures contained 10 μl of SYBR Master Mix, 0.15 μM CBSV primers (0.1 μM for UCBSV and for cassava 4.1_010236 primers), 5 μl of diluted cDNA template, and nuclease-free sterile water to a total reaction volume of 20 μl. Control reactions, non-template water, RNA from healthy cassava, and RNA from UCBSV-infected cassava were included in every reaction series to conduct qRT-PCR with two technical replicates. After an initial denaturation step for 3 min at 95°C, each two-step cycle consisted of denaturation for 10 s at 95°C and synthesis for 30 s at 60°C. PCR was done for 36 cycles followed by melting curve analysis to assess the specificity of the amplification.To confirm presence/absence of U/CBSV in cassava, a one-step TaqMan assay was conducted  with virus-specific primers and probes and COX (cytochrome oxidase) as an internal control . Reactio−ΔΔCt method (Cycle threshold (CT) values were used to calculate U/CBSV expression using the 2t method . Virus eA highly efficient screening and evaluation protocol was prerequisite to test such large numbers of plants for virus infection responses and to identify virus resistance in individual plants. Prior to the virus study, UCBSV isolates representing the core diversity of virus genomes  and haviThe infection processes of U/CBSV reference isolates were followed in the cassava varieties Albert  and Namikonga  for 60 dag by evaluating the onset and severity of symptoms and quantifying virus load in leaves. In the variety Albert, symptoms of CBSV infections became visible already 10 dag, while symptoms of the UCBSV-Ke125 appeared much later and were generally mild and sometimes only barely visible during the first 30 dag .All viruses caused streak symptoms on stems, which became evident on both varieties 60 dag, however, were most severe in CBSV-Mo83 infections. Virus concentrations in leaves fluctuated over time , with hiWhen virus responses of the CBSD-susceptible variety Albert were compared with that of the virus-resistant Namikonga , similarFinally, based on the early expression of symptoms and the rapid accumulation of virus RNA, CBSV-Mo83 was determined as the most pathogenic virus isolate among the CBSVs maintained in the reference virus collection at DSMZ. Consequently, CBSV-Mo83 was selected as inoculum for the initial virus screening.In the virus bioassay, all African cassava lines became infected with CBSV-Mo83 and either were highly sensitive to the virus and responded with wilting followed by plant death or developed severe virus symptoms on leaves and stems. In our virus bioassays, the resistant varieties Namikonga and Kiroba  became iMost of the South American cassava lines were susceptible to CBSV infection and to developing systemic symptoms ranging from vein clearing to wilting and plant death , 6C. SevThe 238 cassava South American cassava lines included in the CBSV-Mo83 bioassay responded to virus infections, with symptoms ranging from wilting followed by plant death to absence of CBSV-Mo83 symptoms .Cassava varieties that remained virus free during the first screening phase were subjected to a second round of screening, during which several candidate accessions became virus infected. However, after two rounds of high stringency screening, 15 cassava lines remained free of virus symptoms, and there was no virus detected.At the end of the bioassay, after 5 to 8 months, when tuberous roots from the 15 apparently virus-free cassava lines from South America were examined, tubers from 8 cassava lines  showed necrosis symptoms, and virus was detected by qRT-PCR . Leaves CBSV-Mo83 infections did not establish in seven cassava lines: DSC167, DSC196, DSC250, DSC258, DSC120, DSC269, and DSC118. All inoculated plants were free of symptoms, and there was no virus detected in all organs and tissues tested .The virus isolates selected for the bioassays were from the three major phylogenetic clades: CBSV, CBSV-Tan70, and UCBSV , and difTo exclude that tissue incompatibility, necrosis, or other barriers would prevent translocation and movement of virus from infected buds into rootstocks, a further virus infection experiment was conducted with DSC167 and the variety Albert as susceptible controls. A chimeric TMS-96/0304 rootstock with a branched canopy, one branch from TMS-96/0304 and the other from DSC167, was infected by grafting CBSV-Mo83 buds to the susceptible rootstock. Virus symptoms became visible 10–14 dag on the leaves of TMS-96/0304 (11 of 12 grafted plants), and systemic virus infections with pronounced symptoms and high virus load developed in the following weeks. In the TMS-96/0304/Albert chimeric plants (six of six grafted plants), virus symptoms became visible on leaves of both branches, and a severe systemic disease developed. In contrast, the DSC167 branches of all chimeric plants remained symptomless throughout, and virus was undetected or below the qRT-PCR detection threshold in stem and leaf tissues taken from those branches . CuttingAfter two cycles of stringent virus screening and approximately 24 months of intense monitoring, 15 cassava lines with resistance against CBSV-Mo83 were identified in the germplasm accessions from South America .High resistance against CBSV-Mo83 was found in seven cassava lines, and those did not become infected with CBSV-Mo83. Additional virus bioassays with CBSV and UCBSV isolates, CBSV-UG65, CBSV-Tan70, and UCBSV-Ke125 provided evidence that virus resistance was also effective against diverse viruses. Virus testing with other cassava accessions are not yet finalized to conclude on their resistance spectrum.Resistance against the viruses causing cassava mosaic and CBSDs is key to cassava cultivation in Africa and, thus, is a vital element of all breeding programs aimed at genetic improvement of this important food crop. Breeding for resistance against Cassava mosaic viruses, causing the most widespread cassava disease on the African continent , has beeM. glaziovii , which was developed during the Amani program  would eventually show root symptoms. Although incidence and severity of root symptoms can be low in those varieties, propagation of cuttings from virus-infected plants (secondary infection) eventually leads to an increase of root symptoms in successive growing cycles and to more severe impact. Thus, in our screening protocol, a cassava variety developing virus symptoms was eliminated from further testing, notwithstanding symptom severity, onset of infection, and virus titer.The challenge of cassava virus resistance testing under laboratory (glasshouse) conditions was to establish an efficient virus infection method that would allow the use of only a few plants of each accession for infection experiments in the first high-throughput screening. We therefore increased the virus infection efficiency to more than 90% by using two axillary buds from virus-infected source plants to infect cassava by grafting. Indeed, this treatment did not only guarantee that almost all plants became infected but also triggered early plant responses because of the high virus inoculum delivered.Considerable differences in accumulation of CBSV and UCBSV in cassava were reported , and virRutacea that are commonly used as rootstocks  genes necessary for precise interaction with host proteins or structures are missing. On the other hand, the resistance phenotype may be the lack of replication or because the phloem cells represent an impermeable physical barrier to prevent passage of the virus to mesophyll cells for replication.Our infection experiments were rigorous and reproducible to provide strong evidence for cassava resistance . HoweverThe screening strategy we chose was based on the reasoning that resistance against the most aggressive virus isolate, CBSV-Mo83, would not only be most efficient to eliminate susceptible lines but may also lead to the identification of broad-spectrum resistance against other U/CBSV isolates. Indeed, in an earlier study, we identified UCBSV resistance in cassava varieties that were otherwise susceptible against CBSV . The resIn field situations, scoring for U/CBSV resistance is problematic because of the uncertainties about (1) the presence and identity of (a) particular virus (es), (2) the infection pressure (whitefly population size), and (3) the time point of infection. These inaccuracies have a severe impact on the entire cassava breeding process and prolong the selection and evaluation to 3–4 years . The curIn this work, we present South American cassava breeding lines that are resistant against CBSV and other viruses encompassing the diversity of viruses causing CBSD. Evaluation of some of the lines grown at several sites in East Africa confirmed that the resistance against both viruses, CBSV and UCBSV, was maintained. While the appraisal is still ongoing, we are confident that these new cassava materials can provide the genetic sources needed to make substantial progress in cassava breeding for CBSD resistance. Finally, this work highlights the invaluable contribution of germplasm collections to supply the genetic resources for the improvement of our crops.SW conceived the project and designed the experiments. SS and BF carried out the experiments and generated the data. SS, BF and SW analyzed the data. SS and SW wrote the manuscript. All authors contributed critically to the manuscript and agreed to the final content.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


EGFR gene.Pneumatosis intestinalis is a rare adverse event that occurs in patients with lung cancer, especially those undergoing treatment with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKI). Osimertinib is the most recently approved EGFR-TKI, and its usage is increasing in clinical practice for lung cancer patients who have mutations in the EGFR gene mutations, namely a deletion in exon 19 and a point mutation (T790 M) in exon 20. Osimertinib was started as seventh-line therapy. Follow-up computed tomography on the 97th day after osimertinib administration incidentally demonstrated intra-mural air in the transverse colon, as well as intrahepatic portal vein gas. Pneumatosis intestinalis and portal vein gas improved by fasting and temporary interruption of osimertinib. Osimertinib was then restarted and continued without recurrence of pneumatosis intestinalis. Overall, following progression-free survival of 12.2 months, with an overall duration of administration of 19.4 months (581 days), osimertinib was continued during beyond-progressive disease status, until a few days before the patient died of lung cancer.A 74-year-old woman with clinical stage IV (T2aN2M1b) lung adenocarcinoma was determined to have Pneumatosis intestinalis should be noted as an important adverse event that can occur with administration of osimertinib; thus far, such an event has never been reported. This was a valuable case in which osimertinib was successfully restarted after complete recovery from pneumatosis intestinalis, such that further extended administration of osimertinib was achieved. Pneumatosis intestinalis is a disease in which air-containing cysts form within the submucosa or serosa of the intestinal tract . AlthougEGFR gene mutation and an acquired drug-resistant mutation, such as the exon 20 T790 M point mutation . –15. 7–15ulations , 28. TheBecause our patient had already experienced six regimens of anticancer therapy, osimertinib was considered to be the singular option that had the potential to stabilize the progression of lung cancer. The restart and continuation of osimertinib under close observation was a meaningful approach, which resulting in the patient maintaining PFS for 19.4 months. Our patient had essentially no underlying risk factors, and the change of the EGFR-TKI from afatinib to osimertinib was the only way in which her condition was altered during the time that pneumatosis intestinalis developed. The absence of recurrence after restarting osimertinib might be explained by the use of dietotherapy that focused on ease of digestion and the avoidance of factors that could have exacerbated pneumatosis intestinalis, such as constipation.Pneumatosis intestinalis is a rare adverse event that can occur in patients with lung cancer treated with osimertinib. In this case, it was a valuable and successful option to restarted osimertinib after the patient had completely recovered from pneumatosis intestinalis without deterioration, resulting in extended administration of osimertinib.


We report here the complete genome sequence of a Sindbis virus (SINV) strain, ArB7761, isolated in 1977 in the Central African Republic. This strain, closely related to the Babanki virus, belongs to the SINV genotype I clade. We report here the complete genome sequence of a Sindbis virus (SINV) strain, ArB7761, isolated in 1977 in the Central African Republic. This strain, closely related to the Babanki virus, belongs to the SINV genotype I clade. However, it differs from the Egyptian prototype strain AR339 by several indels in the nsP3 gene. Alphavirus, a member of the Togaviridae family. In humans, SINV infections are mainly benign, consisting of fever, rash, arthralgia, and myalgia  (The Sindbis virus (SINV) is the prototype of the arthropod-borne virus (arbovirus) genus  myalgia , but no  myalgia . Childre myalgia . This zo Russia) , althougCulex cinereus mosquitoes collected in a forested area in 1977 at Bozo , Central African Republic (CAR). The lyophilized virus was resuspended in phosphate-buffered saline and amplified on Vero E6 cell lines. Cytopathic effects were observed 2 to 3 days postinfection, and then the harvested supernatant was used for RNA extraction using the QIAamp viral RNA minikit (Qiagen). Double-stranded cDNA was synthetized and used for paired-end library construction with the NEBNext Ultra RNA library prep kit for Illumina . High-throughput sequencing was performed on a MiSeq instrument (Illumina). A total of 4,685,922 paired-end reads were obtained, and 195,973 reads corresponded to SINV. Analysis revealed a sequence of 11,709 bp in length. Our sequence shows 99% similarity with the Babanki virus (GenBank accession number HM147984) from Cameroon and 94% similarity with the AR339 prototype SINV strain (J02363). At the amino acid level, similar to most alphaviruses, there is an additional stop codon between genes for nonstructural proteins nsP3 and nsP4. Compared with AR339, five amino acids (codons)  are inserted at positions 1786, 1787, 1788, 1799, and 1800 of the nonstructural polyprotein nsP123, respectively, whereas three amino acids (codons)  are deleted at positions 1827, 1828, and 1829 at the end of nsP3, respectively. These mutations been already demonstrated in other SINV strains (SINV strain ArB7761 was isolated on suckling mice from a pool of In conclusion, these molecular data on our new SINV isolate support the wide distribution of this virus in Africa. However, given our limited knowledge of this virus and the reasons why cases remain limited to a few regions, further studies are required to better understand its transmission cycles.MH212167.The complete genome sequence of SINV strain ArB7761 was deposited in GenBank under the accession number


We assessed Zika virus RNA and select cytokine levels in semen, blood, and plasma samples from an infected patient in South America. Viral RNA was detected in semen >2 months after viremia clearance; cytokine profiles differed in semen and plasma. After viremia, Zika virus appears to become compartmentalized in the male reproductive tract. Before the 2015–2016 outbreak, Zika virus infection had been associated with only mild symptoms. However, the outbreak revealed infection could cause severe clinical manifestations, particularly for fetuses and newborns (https://www.thermofisher.com).To characterize infection in the MRT further, we conducted a longitudinal 6-month study examining Zika virus load and immunologic profile in blood, plasma, and semen in 1 man. The study patient was a 32-year-old immunocompetent white man with an asymptomatic Zika virus infection acquired in South America in January 2016; the control was a healthy 40-year-old white man without risk factors for acute or chronic infection who lived in the same area. We evaluated the concentrations of a select panel of cytokines, including innate immune mediators ; inflammatory factors ; chemokines ; hematopoietic factors ; the angiogenic factor vascular endothelial growth factor A (VEGF-A); and proteases . We quantified cytokines using ProcartaPlex Multiplex Assay  and RealStar Dengue and Chikungunya RT-PCR Kit 2.0 . The patient did not experience other genital or urinary tract infections during the study.At admission, the patient had moderate fever, maculopapular rash, myalgia, and arthralgia and recovered within a few days. He was HIV negative; dengue and chikungunya virus infections were ruled out using ELISA Diapro  than in blood (9.4 × 103 copies/mL); RNA was detectable for up to 100 days in blood and 168 days in semen (Two days after symptom onset, viral RNA was higher in semen (1.04 × 10in semen . SolubleOur data revealed higher amounts of and more prolonged viral RNA shedding in semen than in blood. Zika virus infection altered cytokine secretion and induced distinct profiles in the plasma and semen; changes in the semen were more prominent. The discrepancies in kinetics and concentrations of cytokines and virus titers between semen and plasma suggest virus compartmentalization.Cytokines produced in the MRT reflect local immune status, organ function, and tissue damage. The high levels of proinflammatory factors in semen samples from this patient illustrate an exacerbated local immune response established to control Zika virus infection. This response might lead to recruitment of more host and inflammatory cells that further amplify viral replication and organ injury (The different kinetics of virus replication and cytokine secretion in semen samples raises questions about the semen secretome in cases of couples aiming for conception and the necessity to extend the convalescence period beyond Zika disease recovery. In fact, at high concentration, most of these factors might alter the integrity of the mucosal barriers within the female reproductive tract and increase a woman’s susceptibility to infection (The limitations of our study include small sample size. Further investigations with a larger cohort of patients and controls warranted.In summary, a profound disruption in the cytokine network is evident in plasma and semen starting at the earliest stage of Zika virus infection and is maintained over time even after viral clearance. Studies to characterize the mechanism involved in the establishment of compartmentalization and develop efficient antiviral therapies that interfere with virus replication in the MRT are needed.


Many viruses of agricultural importance are transmitted to host plants via insect vectors. Characterizing virus–vector interactions at the molecular level is essential if we are to fully understand the transmission mechanisms involved and develop new strategies to control viral spread. Hitherto, insect proteins involved in virus transmission have been characterized only poorly. Recent advances in this topic, however, have significantly filled this knowledge gap. Among the vector molecules identified, cuticular proteins have emerged as key molecules for plant virus transmission, regardless of transmission mode or vector considered. Here, we review recent evidence highlighting that the CPR family, and particularly RR-1 proteins, undoubtedly deserves special attention. Current Opinion in Virology 2018, 33:137–143Virus-vector interactionsThis review comes from a themed issue on Anna E Whitfield and Ralf G DietzgenEdited by Issue and the EditorialFor a complete overview see the Available online 20th September 2018https://doi.org/10.1016/j.coviro.2018.07.015http://creativecommons.org/licenses/by/4.0/).1879-6257/© 2018 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license  that are able to move from plant to plant ,2. The mNonetheless, considerable efforts have been made to develop complementary approaches and high-throughput methods to help identify vector proteins involved in virus–vector interactions. Among these interacting molecules are several cuticular proteins (CuPs) , 25, 26.Potyviridae, Bromoviridae and Caulimoviridae, is retained in the stylets [in vitro interaction assays on dissected stylets, Uzest et al. [Noncirculative viruses bind reversibly to specific retention sites on the cuticle of the feeding apparatus. Therefore, virus-interacting molecules should be cuticular compounds that fulfill the role of virus receptors. To date, receptors of foregut-borne viruses have been poorly characterized ,35, and  stylets , 37, 38, stylets . Using it et al. • in an at et al. . Howeveret al. [Dombrovsky et al.  were theet al. ). A far-et al. ••,25,40•Myzus persicae CuPs [in vitro (Two independent studies on cucumber mosaic virus (CMV) receptor candidates were published in 2017 ,25. Thiscae CuPs , the RR-cae CuPs ••, see bcae CuPs •, was dein vitro . As thesM. persicae via RNA-mediated interference resulted in a 40% decrease in CaMV transmission efficiency.A recent study has made great strides towards noncirculative virus receptor identification ••. By imTo date, the only CuPs identified in insect stylets are proteins from the CPR family ••,25,40•Since circulative transmission entails crossing several vector tissues and travelling within the insect body, various vector molecules are likely to interact with circulative viruses throughout their journey to, firstly, promote virus entry into, and release from, insect tissues, secondly, facilitate virus movement, thirdly, protect viruses from degradation within the insect hemolymph, and lastly, play a role in virus replication in the case of propagative viruses. In addition to classical methods such as YTH screenings, current attempts to characterize insect partners of circulative viruses often rely on the development of high-throughput approaches such as proteomic and transcriptomic analyses able to detect changes in protein abundance or genes differentially expressed between viruliferous or healthy insects. Generally, these studies generate listings with many protein candidates, including some CuPs , 47, 48.et al. [M. persicae were revealed by far-western blot analyses, and a CuP of 33 kDa was identified from 2-dimensional gel electrophoresis and mass spectrometry analysis , and thanalysis . This Cuanalysis  — a protanalysis . Additioanalysis , preclud R. padi , and sec R. padi . Interes3647865, ••). AlthLaodelphax striatellus in a propagative manner [in vivo by a co-immunoprecipitation assay. Moreover, the two proteins co-localized in insect cell culture, and in hemocytes isolated from the hemolymph of viruliferous insects  •• — a tee manner . The aut insects , whereasy glands ••. Two ay glands . These Cy glands .et al. [Aedes aegypti pupae upon infection by West Nile (WNV), dengue (DENV) or yellow fever (YFV) viruses. Overexpression of this CuP gene in mosquito cells or in live mosquitoes inhibited WNV infection. Furthermore, this pupal CuP interacted with the envelope of WNV, DENV and the capsid of YFV, which might impede viral entry to host cells. More importantly, pre-incubation of WNV with pupal CuP prevented lethal WNV encephalitis in mice. This work highlights once again the key role of a CuP from the CPR family in virus transmission through a direct virus–vector interaction. However, in contrast to vectored plant viruses for which CuPs have been shown to promote virus transmission, chitin-binding proteins were instead proposed to protect the insect from viral infection by preventing virus–receptor interactions, or by strengthening natural barriers to pathogen infection.Interestingly, CuPs have also been reported to potentially interact with arboviruses, but the precise role of CuPs in arboviruses infection is not well documented. A deregulation of CuP gene expression in insects upon infection with animal viruses has been reported ,54••,55.Cuticular proteins now feature prominently on the shortlist of insect molecules demonstrated to play a key role in plant virus transmission ••,15••. Almost all the CuPs identified so far in plant virus–vector interaction studies belong to the large CPR family. More precisely, while the role of RR-2 proteins in virus transmission remains to be determined, RR-1 proteins are definitely associated with circulative and noncirculative virus transmission. Future research should help define whether additional CuPs also participate in the transmission process.The data presented in this review highlight the interest in strengthening further efforts to characterize insect CuPs and their interactions with plant viruses. In the future, we can count on growing interest from virologists to characterize CuPs, as novel candidates in the search for innovative viral control strategies.Nothing declared.• of special interest•• of outstanding interestPapers of particular interest, published within the period of review, have been highlighted as


Paramecium bursaria Chlorella virus 1 (PBCV-1) had been the largest known DNA virus, both in terms of particle size and genome complexity. In 2003, the Acanthamoeba-infecting Mimivirus unexpectedly superseded PBCV-1, opening the era of giant viruses, i.e., with virions large enough to be visible by light microscopy and genomes encoding more proteins than many bacteria. During the following 15 years, the isolation of many Mimivirus relatives has made Mimiviridae one of the largest and most diverse families of eukaryotic viruses, most of which have been isolated from aquatic environments. Metagenomic studies of various ecosystems (including soils) suggest that many more remain to be isolated. As Mimiviridae members are found to infect an increasing range of phytoplankton species, their taxonomic position compared to the traditional Phycodnaviridae  became a source of confusion in the literature. Following a quick historical review of the key discoveries that established the Mimiviridae family, we describe its current taxonomic structure and propose a set of operational criteria to help in the classification of future isolates.Since 1998, when Jim van Etten’s team initiated its characterization,  Acanthamoeba-infecting microbe, dubbed Bradfordcoccus, was unsuccessfully investigated as an intracellular parasitic bacterium, resisting all standard characterization approaches. The difficulties, however, were not technical but epistemological [bona fide virologist was ready to make. It was thus for a team of bacteriologists to identify Mimivirus as the first “giant” virus, which then allowed the subsequent discovery of many more of them that now encompass at least four different families and have opened a new and booming era in virology [The viral nature of Mimivirus was finally recognized in 2003 ,2, more ological ,5. Aftervirology .Mimiviridae a prominent family among aquatic viruses , with small round cells that are 3 µm in diameter and are nowadays quite popular as a detoxifying nutritional supplement in health food stores. Ironically, Chlorella are linked with the history of virology from the very beginning, since they were discovered by the same famous Dutch microbiologist Martinus W. Beijerinck, who coined the term “virus” (even though its concept of “liquid” infectious agent was quite wrong) [Chlorella-infecting viruses instead of simply reproducing Ivanovsky’s work on the filterable tobacco mosaïc virus [The saga of giant viruses truly began with the pioneering work of Jim van Etten and his collaborators who discovered, isolated, and extensively characterized the first large DNA viruses infecting a protist. This protist was the unicellular freshwater green algae e wrong) . Thus, wïc virus . No doubïc virus  and the Chlorella were published in 1981 [The first descriptions of very large icosahedral viruses infecting  in 1981 ,32, whic in 1981 . An inte in 1981 , thus coChlorella of paramecium , its characterization proceeded quickly. Much before the completion of its genome sequencing in 1997 [Chlorella viruses as “very large” instead of giant. As we progress in our knowledge about their structure and metabolic capacity, it becomes clear that no fundamental biological difference distinguishes very large from giant dsDNA viruses that even coexist in the same Mimiviridae family.Once Van Etten and collaborators realized that the easiest virus to work with was one infecting a symbiotic  in 1997 , they co in 1997 . The sta in 1997 . Histori in 1997 , then ag in 1997 . Followi in 1997 ,3,4, JimMegavirus chilensis, from water sampled off the coast of central Chile [Mimiviridae members, M. chilensis infects Acanthamoeba, i.e., the original laboratory host of Mimivirus. With its 1.26-Mb genome predicted to encode 1120 proteins, M. chilensis remained the largest Acanthamoeba-infecting Mimiviridae until the recent isolation and characterization of two new aquatic isolates called Tupanviruses [Our determination of the complete genome sequence of Mimivirus in 2004 . The secal Chile . In contnviruses  , a 2–6-μm-long bicosoecid heterokont phagotrophic flagellate (Stramenopiles) that is widespread in marine environments [C. roenbergensis virus suggested the existence of a distinct clade within the Mimiviridae [Acanthamoeba and C. roenbergensis), belonging to the earliest diverging branches within the Eukaryota, the unikonts, and the bikonts [Acanthamoeba-infecting Mimiviridae, CroV’s particle is only 300 nm in diameter. Yet, its 693-kb genome (predicted to encode 544 proteins) remained the largest of all marine plankton-infecting viruses until recently , Phaeocystis pouchetii and P.globosa , and Chrysochromulina ericina  [Mimiviridae. Such a clade was clearly confirmed following the analyses of the complete genome sequences of P. globosa virus (PgV) in 2013 [Aureococcus anophagefferens virus in 2014 [C. ericina (now Haptolina ericina) virus (CeV) in 2015 [Mimiviridae was recently extended to bona fide green algae  with the detailed characterization of a virus (TetV) infecting Tetraselmis [Mimiviridae , Pelagophyceae (AaV), and Chlorodendrophyceae (TetV)).Prior to the complete genomic characterization of Mimivirus, a number of viruses infecting various species of unicellular algae had been isolated. These viruses exhibiting large dsDNA genomes packed in large icosahedral particles were propagated on cultures of phyceae) ,53,54. Tphyceae)  or capsiphyceae)  produced in 2013 , of Aure in 2014 , and C.  in 2015    and Tupanvirus deep ocean (TupanDO) (isolated from 3000 m deep marine sediments), can be propagated in the laboratory on A. castellanii and Vermamoeba vermiformis [Bodo saltans virus (BsV), exhibiting a 1.39-Mb genome predicted to encode 1227 proteins. Interestingly, both types of viruses hint at the existence of further subdivisions in the growing Mimiviridae family —curiously shared with the octocoral mitochondria —was recoironment .Mimiviridae members based on two large contigs assembled from environmental sequences. Their claim was further supported by the full genome assembly of a virophage, then known as a unique parasite of Mimivirus [Chrysochromulina and Phaeocystis. Like other algae-infecting Mimivirus relatives, these viruses are now believed to define a Mimiviridae subfamily  in the ocean, although most of the sequences classified in this family showed a large divergence from known viral genomes. This suggests that we need more isolates to adequately span the diversity of the family  predicted to be part of the same genome by a heuristic bioinformatics procedure called “binning”. A similar uncertainty is shared by three other predicted Klosneuvirus relatives . Despite the lack of physical isolates, the authors have proposed to classify them in a new subfamily (the “Klosneuvirinae”) within the family Mimiviridae. Fortunately, the isolation of BsV  truly unmatched among known (aquatic) viruses.The latest unexpected addition to the family lvescens , called lvescens . There ilvescens ,79. OnceMimiviridae can be found erratically classified as members of the Phycodnaviridae family in the genus Prymnesiovirus (PgV) as “unclassified Phycodnaviridae”  or as “unclassified virus” (TetV-1). Among partially sequenced Mimiviridae candidates (inferred from metagenomics assemblies), the naming and classification of two “Organic Lake Phycodnaviruses” (OLPV-1 and OLPV-2) has been particularly misleading. Others include Phaeocystis pouchetii virus (PpV-01) and Pyramimonas orientalis virus (PoV-01B). These erroneous classifications are not detected by nonspecialists and do affect the outcome of automated large-scale phylogenetic analyses and gene content comparisons, such as the delineation of core gene sets.The discovery of an increasing number of Mimivirus relatives infecting algae has generated some confusion in the literature about their taxonomic assignment. This confusion is propagated through the nonofficial classification assigned to their associated genomic entries by leading reference databases such as NCBI . CompletPhycodnaviridae family. According to its official ICTV definition, the family is meant to include algae-infecting viruses with large icosahedral virion (Ø > 100 nm) and large genome (>100 kb). The family was then further divided into five genera based on the algal host  is a good example of this problem. Two types of very different dsDNA Prymnesioviruses have been shown to infect the unicellular algae Phaeocystis [Mimiviridae [Haptophyceae-infecting viruses and the so-called Organic Lake “phycodnaviruses” [Phycodnaviridae family includes a “Coccolithovirus” genus corresponding to a third type of virus infecting Emiliania huxleyi that is also a Prymnesiophyceae. Thus, even within a single host genus, the current partition does not correctly reflect the diversity of the “Phycodnaviridae”. More problems can be anticipated with the green dinoflagellate Heterocapsa circularisquama (Dinophyceae), infected by a large DNA virus which might be close to the Asfarviridae [The current genus partition, designed according to the taxonomy of the algal host, is similarly unsatisfactory, as it suggests a one-to-one correspondence between virus and host type, which we know is obviously wrong . The diversity of the viruses infecting the eocystis . This iseocystis  . These key properties/proteins will be linked to a similar structure of the virion , the genome replication machinery (DNA replication and repair enzymes), the virus cycle dependency of nuclear functions , or the intracellular location  of particle production. Proteins/enzymes uniquely present in a group of viruses will be particularly useful as family “signature” even though they will be useless in the context of broader phylogenetic analyses. Finally, we do expect that the physiological traits shared by these viruses will make their global gene contents qualitatively similar. Members of the same virus family should then appear well clustered in a cladistic analysis/tree ,62.Mimiviridae complete genome sequences is now large enough to make each new member easily recognizable by global protein level similarity searches. Even though the four most recent Mimiviridae isolates  exhibit a variable fraction of predicted protein best matching viral database entries, more than 60% are from previously characterized members of the family.The number of available Mimiviridae candidates in the phylogenetic trees built from sequence alignments or key enzymes such as B-type DNA polymerase, virion packaging ATPase, major capsid protein , and three types of proteins  with homologs in other families of large dsDNA viruses [Confirmatory evidence is readily provided by the positioning of  viruses .Mimiviridae members led to the discovery of various key features apparently unique to the family. The association of any of them with a candidate virus  will considerably strengthen its tentative classification as a new member of the Mimiviridae. These key findings include:AAAATTGA motif in the promoter regions of early transcribed genes [A high prevalence of the strictly conserved ed genes .A high prevalence of hairpin-forming transcription termination motifs in the 3′ end of genes .Mimiviridae [The co-isolation (or sequencing) of a virophage. Virophages are small dsDNA viruses with 17–18-kb genomes that can only replicate in host cells undergoing an infection by iviridae ,87. Not The detection of a transpoviron. Transpovirons are 7-kb-long plasmid-like linear dsDNA molecules found in association with Mimivirus-relatives .Mimiviridae-specific version of glutamine-dependent Asparagine synthetase (AsnS). A different, easily distinguishable homolog of this enzyme is encoded by some Prasinoviruses  [The presence of a gene encoding a ., OtV5) .Mimiviridae, although not unique to them anymore [Mimiviridae members (from 0 up to 20 different ones in Tupanviruses [Mimiviridae.The presence of amino-acyl tRNA synthetases (aaRS). The finding of such central components of the translational apparatus in the Mimivirus genome  was cons anymore . Unfortunviruses ) . MutS proteins are ubiquitous in cellular organisms. However, the Mimiviridae MutS7 version is curiously related to the one found in ɛ-proteobacteria and in the mitochondrial genomes of octocorals , Haptophyta (PgV), Chlorophyta (TetV), Excavata (BsV), Heterokonta (CroV), and perhaps Opisthokonta (Sturgeon virus). In addition to its host diversity, the Mimiviridae family is also the one exhibiting the broadest distribution of genome sizes (from 370 kb for AaV to 1.51 Mb for TupanDO) as well as of particle sizes . Despite these huge differences, all currently known members of the family appear to propagate in particles with similar architecture  and replicate in the host cytoplasm using their own well-conserved transcription machinery. Yet, their gene contents are also extremely variable, the intersection of which only amounts to 30 strictly conserved core genes [Mimiviridae family into smaller more homogenous distinct families, as we suggested for the Phycodnaviridae.Fifteen years after the publication of its prototype Mimivirus, the  viruses . Retrospre genes . Future


Nipah disease is a highly fatal zoonosis which is caused by the Nipah virus. The Nipah virus is a BSL-4 virus with fruit bats being its natural host. It is mainly prevalent in Southeast Asia. The virus was first discovered in 1997 in Negeri Sembilan, Malaysia. Currently, it is mainly harmful to pigs and humans with a high mortality rate. This study describes the route of transmission of the Nipah virus in different countries and analyzes the possibility of the primary disease being in China and the method of its transmission to China. The risk factors are analyzed for different susceptible populations to Nipah disease. The aim is to improve people’s risk awareness and prevention and control of the disease and reduce its risk of occurring and spreading in China. The Nipah virus (NiV) belongs to the paramyxovirus family and the Henipavirus genus. In addition to thia, the Henipavirus genus also has four virus members: the Cedar virus (CedV), Kumasi virus (KV), Mòjiāng virus (MojV) and Hendra virus (HeV) ,2. Due tHenipaviruses are lipid-encapsulated viruses that form spherical to polymorphic, sometimes filamentous, particles. Wrapped in the virus particles is the filamentous nucleocapsid, which is made of viral RNA and nucleoproteins, and is associated with the RNA-dependent RNA polymerase and phosphoprotein  The diamNiV was first discovered in the state of Negeri Sembilan in Malaysia in 1997  and was From 2001 to 2015, there were reports of outbreaks of NiV in Bangladesh in almost every year . There wCurrent research indicates that fruit bats of the Pteropus genus are the natural hosts of NiV . They arIn the first outbreak of NiV in Malaysia in 1998, pigs played a very important role as intermediate hosts . The pigHumans are infected with NiV mainly through contact with the secretions and body fluids of infected pigs and humans, or by corpses. In the epidemic of NiV in Malaysia, the diseased population was mainly infected with NiV after exposure to secretions of sick pigs . Among tAs the main disease populations of Nipah disease, the clinical symptoms of pigs and humans are the most typical. Pigs infected with NiV mainly show acute febrile disease, including dyspnea, increased salivation, and serous or bloody pus in the nasal cavity, in addition to neurological symptoms such as delirium and epilepsy, nystagmus, and obvious paralysis symptoms. In humans, the main organs affected by the Nipah virus are the brain and lungs . PatientThe HeV-infected hamster model indicates that the virus is transmitted by direct contact, rather than by aerosol . The zooIn Bangladesh, the most common route of infection is through the consumption of raw date palm sap contaminated with fruit bat urine or saliva, especially in Western Bangladesh ,39. In lLivestock feeding on wild fruits contaminated by bats with NiV can be infected with the virus, and the infected animals further spread the virus to other animals, including humans. Pigs are infected with NiV after swallowing fruit buds or saliva-contaminated fruits. In 2014, the Philippines reported an NiV incident. The outbreak in the Philippines was likely caused by the Nipah virus. In this incident, 17 people were infected, nine died, and the death rate was 53% . AlthougThere are many types of bats with 188 species from 42 genera. In addition, there are 59 species of fruit bat in the Pteropodidae ,48. FruiBy using In Hainan, Guangxi and other places in Southwestern China, there are fruit bats which are the natural host of the Nipah virus. In these areas, pigs are mainly raised free range, which presents the risk of human infection with the Nipah virus through pigs infected by fruit bats. Moreover, China imports a large number of pigs from abroad every year, and there is also the risk of Nipah disease being introduced into China. Because of the ease of spread and high lethality of Nipah disease, it is necessary to conduct a risk analysis on the outbreak of Nipah disease in China.With the continuous development of China’s economy, China has traded with foreign countries more frequently and inevitably trades with the Nipah disease countries. According to reports, among the neighboring countries bordering China, Nipah disease has also occurred in Siliguri, India . AlthougPigs are important intermediate hosts in the outbreaks of NiV in Malaysia . The outWith the improvement of the economic level and the increasing convenience of transportation, the number of tourists from Southeast and South Asia to China has gradually increased. At present, some institutions in China have initially established real-time quantitative RT-PCR methods and indirect ELISA methods for the detection of Nipah virus, which are used to prevent the introduction of Nipah disease, but they ignore the possibility of China being a source of the disease. As shown in The natural host of the NiV is fruit bats of the genus Pteropus (“Flying bat”) . Fruit bDue to the increase in large-scale breeding of pigs in China and the promulgation of the ecological pig raising policy in recent years, the small- and medium-sized pig farms have been strongly affected. According to the China Animal Husbandry Yearbook statistics, during the period 2008–2014, the number of pig farmers in the country decreased by 22.845 million in six years. However, the small and medium-sized pig farms have not disappeared as yet. The owners of small-scale farms who have sold less than 500 pigs in a year still account for 99.6%, and the number of slaughtered pigs accounts for 58.2% of the total number of 735 million heads in the country . This inChina’s Guangxi, Hainan, Yunnan, and other regions are rich in longan, lychee, banana, mango, pineapple, and other fruits and wild fruits—foods eaten by fruit bats. Brown fruit bats also like to suck sugar cane, kapok, nectar, and other sugar-rich fruits in winter . Every yIn Bangladesh, there have been cases of infection with NiV due to drinking fresh date palm sap . In the China should pay attention to this emerging zoonosis. Although it was confirmed that ribavirin inhibits the replication of Nipah virus in vitro, it was found to have a therapeutic effect by a small number of patients and hamster model infection experiments . While a