The molecular imprinting polymers (MIPs) have shown their potential in various applications including pharmaceuticals, chemical sensing and biosensing, medical diagnosis, and environmental related issues, owing to their artificial selective biomimetic recognition ability. Despite the challenges posed in the imprinting and recognition of biomacromolecules, the use of MIP for the imprinting of large biomolecular oragnism such as viruses is of huge interest because of the necessity of early diagnosis of virus-induced diseases for clinical and point-of-care (POC) purposes. Thus, many fascinating works have been documented in which such synthetic systems undoubtedly explore a variety of potential implementations, from virus elimination, purification, and diagnosis to virus and bacteria-borne disease therapy. This study is focused comprehensively on the fabrication strategies and their usage in many virus-imprinted works that have appeared in the literature. The drawbacks, challenges, and perspectives are also highlighted. Viruses are not always the harmful species as they do offer many useful possibilities in biomedical and bionanotechnological applications, anti-microbial agents, synthesis of vaccine, preparation of food materials. Despite their beneficial characteristics, the term viruses can often cause havoc in the general population due to some immensely emphasized deadly diseases such as Corona, Dengue, Avian influenza A H7N9 virus, Severe Acute Respiratory Syndrome (SARS), Hepatitis, Ebola, and Acquired Immunodeficiency Syndrome (AIDS) leading to high mortality and morbidity rates. It can be argued that there are more negative effects than beneficial ones ,2.Viruses are responsible for a number of deadly outbreaks in humans and livestock. These diseases may be due to waterborne viruses where the virus is transmitted through the consumption of unsafe and contaminated harmful biological agents. According to the 2017 WHO/UNICEF Joint Monitoring Program (JMP) report, approximately 2.1 billion people do not get clean, readily available water at home, and 6 in 10 or 4.5 billion people do not have access to safe, readily accessible water at home. In addition, the WHO study also points out that at least 2 billion people worldwide use a faeces-contaminated drinking water that is considered, as one of the potential paths of pathogenic human enteric viruses’ infection among masses . AccordiViruses include virions made up of protein coat encapsulated DNA or RNA genome that use various mechanisms to transport genetics to regulate the host cell’s artificial machinery for viral proliferation. Furthermore, since viruses are highly resistant to normal surrounding conditions , they multiply in vast quantities, posing serious threat to healthy organisms. These issues compelled researchers to investigate the fast, effective, and timely detection and diagnosis of viruses for pandemic control and prevention. The literature revealed that there are many outstanding procedures available for the successful diagnosis of virus infections. For example, quartz crystal microbalance (QCM) , polymerIn the last 2–3 decades, several efforts are being made to prepare synthetic materials in which molecularly imprinted polymers (MIPs) have displayed their peculiar and impressive characteristics, such as their intense affinity, high selectivity, good stability, and reliability in a hostile environment of synthesis and analysis. MIP creates template-shaped cavities in polymer matrices with memory of the template molecules which is similar to “lock and key” method, and one can design a kind of artificial antibody materials that are able to re-interact noncovalently with the imprinted analyte ,21,22,23There have been a few review papers on virus identification over the last decade. For example, Rijn and Schirhagl  discusseEscherichia coli and is a member of family Leviviridae. The development of a “Fr” bacteriophage imprinted polymer for the prevention of anti-viral infection was demonstrated by Sankarakumar and Tong [A bacteriophage, also known as phage, is a virus that infects and reproduces inside a bacterium. The “Fr” is an enteric phage that resides within and Tong . For theand Tong  develope−9 M with a LOD value of 5 × 106 pfu·mL−1. In addition, cross-reactivity evaluation with other viruses or analytes such as vancomycin and QB phage using the SPR sensor demonstrated the promising behavior of nanoMIP for selective virus determination.Altintas et al.  proposedAdenoviruses are medium-size virus causing cold, bronchitis, diarrhea, and urinary bladder infection, etc. They are composed of double-stranded DNA genome. Altintas and co-workers  developeThe Dengue virus, one of the most feared mosquito-borne viruses, specifically targets humans and primates and can cause a particular form of hemorrhagic fever called dengue fever. It has shown its deleterious effects in developing countries since last decade. The Dengue fever demands urgent and accurate diagnosis due to its rapid and fatal infections just after 4 days of fever onset. Furthermore, 1 of the 4 antigenically different dengue virus types is the main cause of infection and the infection from virus does not provide cross-protective immunity against the others. Therefore, practitioners need to be particularly vigilant in order to diagnose the difference between primary and secondary dengue virus infections ,45,46.N-benzylacrylamide via UV irradiation onto a QCM chip. The average thickness of polymeric thin film was estimated to be 70 nm. The comparison between epitope imprinted polymer and protein surface imprinting polymer showed that both the template and the proteins  that had the same epitope part of the structure were effectively identified by the polymers imprinted with a peptide. This approach achieved a corresponding frequency change in QCM chips immobilized with Dengue virus monoclonal antibodies. To realize the application of above-mentioned method, Tai group [The first MIP based imprinting for dengue virus was performed by Tai group , where aai group  tested tai group  demonstrThe avian virus poses a serious threat to mammals, including humans, to a large degree, as common avian virus variants can lead to avian H5N1 strains that are more likely to infect mammals widely ,51. AmonWangchareansak and co-workers  were the−1 was achieved.A. Selectivity studies indicate that MIPs were selective towards the corresponding virus template and LOD as low as 105 particles·mLThe same group  used theThe binding of H5N1 to the polymer was reported to be strongly inhibited by oseltamivir compared to anti-H5, which in turn is more effective than sialic acid. These experimental findings are promising because they can discern conformational effects from small inhibitors and substrates to macromolecules. Despite the good selectivity, both of these methods were tedious in terms of preparation and assay of the imprinted polymer. Karthik et al.  suggeste8 virus particles·mL−1 for poliovirus that was comparable to template solution of 3880 × 108 virus particles·mL−1 (0.644 nM).Poliovirus is one of the most harmful viruses causing poliomyelitis, a crippling and potentially deadly infectious disease, which mainly affects young children. The disease causes partial paralysis that is often permanent and cannot be cured . Hence, 2 nanoparticles via one-step synthesis method as shown in HAV is responsible for serious liver disease by consumption of contaminated foods and water or by direct contact with an infected individual. Acute HAV infection is hard to differentiate from other types of Hepatitis infections and influenza infection, thus accurate and specific diagnosis is a needed . Cai gro−1 and LOD of 8.6 pmol∙L−1 were obtained. The sensor was very selective toward HAV compared to other viruses such as rabies vaccine, Japanese encephalitis (JEV), and the mixture of measles vaccine and rubella vaccine. In addition, it could identify HAV from a 20,000-fold diluted human serum sample. Cai and coworkers [Improved RLS intensity corresponding to HAV concentration from 0.04 to 6.0 nmol∙Loworkers  synthesi−1 with in 20 min. A reasonable recovery of 88% to 108% of HAV from HAV spiked human serum samples was obtained. The determination of HAV and HBV (Hepatitis B virus) is challenging owing to their similar structures. Hence, the Cai group [Recently, Cai and co-workers  fabricatai group  proposedJEV is a mosquito-borne zoonotic pathogen of severe concern because it causes Japanese Encephalitis (JE), which is a neurotrophic killer disease, which, in turn, is responsible for viral acute encephalitis syndrome (AES) globally. Cai group worked in this area and reported 2 different protocols to determine JEV via imprinting method.In their first report, a surface imprinted fluorescent sensor using JEV with magnetic silicone micro-spheres acting as carrier materials and tetraethyl orthosilicate (TEOS) and 3-aminopropyl triethoxysilane (APTES) functioning as building blocks was proposed. The sensor provided an imprinting factor of 2.98. Moreover, sensitive fluorescent detection in water with a good linearity within 2.5–45 nM, and a detection limit of 0.32 nM with excellent selectivity of JEV in 1000-fold dilution of human serum sample solution was achieved . JEV imp−1 and 0.11 pM of LOD was achieved for JEV. The sensor showed larger quenching toward JEV as compared to other virus species such as HAV, SV40, and Rabies virus and offered recoveries between ~98–100.56% in spiked human serum samples.In order to synthesize JEV imprinted fluorescence sensor on silicon-modified metal organic frameworks using zinc acrylate as a functional monomer, the Chen and Cai group  exploredApple stem pitting virus (ASPV), a widespread plant pathogenic virus. Via a dual imprinting method, Bai and Spivak  develope−1, which was in close agreement to the results obtained from ELISA or fluorescence-tag systems.The sensor was capable of detecting the ASPV by simple laser transmission equipment up to 10 ng·mLSome of the significant human and animal pathogens belong to the picornavirus virus family. For instance, human rhinovirus (HRV) or the foot-and-mouth-disease virus (FMDV) are two typical examples of Picornaviruses and they have common icosahedral shape with an outer protein capsid and an RNA strand in their centers. There are nearly 100 major stereotypes of HRV. Therefore, synthetic recognition materials are required not only to determine HRV, but also to distinguish between different serotypes.Jenik et al.  exploite−1. Furthermore, the imprinted cavities were capable to differentiate the various stereotypes and types of virus with high selectivity. Hussein et al. [−1 that was 50 times lower than the ELISA and PCR in the analysis of saliva real samples. The biosensor offered good selectivity toward FMDV serotype O over all other genus serotypes A, SAT2, Lumpyskin disease virus (LSDV), and inactivated serotype O.The QCM measurements demonstrated that sensor yielded excellent signal (−300 Hz) in a virus suspension of ∼100 μg·mLn et al.  preparedTomato bushy stunt virus (TBSV) and turnip yellow mosaic virus (TYMV) are non-enveloped, icosahedral, single-stranded RNA plant viruses. Cumbo and co-workers ,72 targeA well-studied and characterized plant virus, tobacco mosaic virus (TMV) is discussed in this section. Many researchers used TMV as a model virus for their studies due to its robust nature, which can resist any conformation and activity change even after being subjected to harsh environmental conditions .−1 TMV solution clearly showed the impact of imprinting. Moreover, acrylate polymer layer performed better than the polyurethane polymer layer. The imprinted polymers exhibited good selectivity toward TMV in the presence of human rhinovirus serotype-2 (HRV-2) as observed in QCM studies.Hayden et al.  explored−1 polymer) relative to non-imprinted hydrogels (4.2 mg TMV g−1 polymer) in batch experiments. In another study, Bolisay and co-workers [w/v poly (PAA)/TMV) concentration avoided the polymer-virus aggregation as compared to less than 0.0001% w/v concentration. Secondly, 1 M NaOH performed better among several washing methods, such as H2O, 1 M NaCl, 1 M NaOH, and 6 M Urea. Optimized TMV MIPs synthesized by these findings exhibited a strong affinity to TMV (printing factor 2.3) and a poor binding to tobacco necrosis virus (TNV), the non-target virus. In the presence of a template virus in an optimized protocol, Bolisay and Kofinas [−1 TMV solution with 35 mm·s−1 fluid flow was used. This method offered excellent sensitivity until 4 mg·mL−1 (1000-fold decrease) of TMV solution and the imprinted MIP cavities could successfully differentiate HRV2 samples despite similarities in TMV and HRV stereotypes. Bolisay et al.  followed-workers  improved Kofinas  used mor Kofinas  for cont−1 (0.15–15 pg) and exhibited a LOD of 2.29 ng·L−1 (3.4 pg). The response time was just 2 min with high selectivity as negligible fluorescence response for TMV obtained for 10 ng·L−1 sample solution. Moreover, the sensor showed satisfactory recovery of TNV in spiked water samples with standard deviation less than 3.5%.To overcome the hurdles of polymer-virus aggregation and virus removal from polymer matrix, Ikawa and coworkers  immobiliHuman Noroviruses are known for causing severe gastroenteritis infections . The corPestivirus genus. The World Organization for Animal Health (OIE) has categorized this as a threat to the international export of pork around the globe [−1 and the selectivity factors of 2 over porcine respiratory and reproductive virus (PRRSV) and 62 over pseudorabies virus (PRV) were achieved.Classical swine fever (CSF) is one of the extremely infectious viral diseases caused by classical swine fever virus (CSFV), a member of the he globe . Klangprhe globe  developeFlaviviridae family. Generally, it is not known to be much dangerous, but recent reports of a heightened incidence of microcephaly in infants born to women infected with ZIKV during pregnancy have led to concern in the identification and analysis of ZIKV. Tancharoen et al. [−4 pfu·mL−1 (1 RNA copy·mL−1). In addition, the LOD in the presence of dengue virus was eastimated to be 2 × 10−2 pfu·mL−1.Zika virus (ZIKV) is a member of the n et al.  developeIn the above section, we have comprehensively discussed various fabrication approaches for the accurate, selective, and sensitive determination of viruses. Despite many exemplary ways, the road of virus detection seems full of hurdles and challenges. For example, techniques which do not involve extensive equipment or specialized staff are desperately needed, particularly if the findings can be interpreted by the unaided eye, which could significantly lower the cost of manufacturing. Unfortunately, there are only a few works performed where visual detection of the virus was explored (68). Miniaturization and portability are another crucial need of the time when patients may be given point-of-care diagnosis. The incomplete removal of the polymer matrix and sluggish mass transfer kinetics is one of the most significant problems in large imprinting biomolecules. Using surface imprinting, these problems were alleviated, but their solutions introduced laboriousness and arduousness into the fabrication processes ,88. SomeDuring the current COVID-19 crisis, one of the biggest challenges is the accurate and reliable COVID-19 diagnostics. While there have been reports, even commercial efforts, that highlight the use of immunosensors to create fast test alternatives for the routinely used PCR analysis ,90,91, nDespite many challenges ahead, the MIP technique is attractive and increasingly utilized in virus imprinting as it is evident from many works that yield highly selective customized cavities. They are cost effective and could stand a harsh environment with outstanding stability and reusable artificial receptors. We could safely assume that MIP is going to play pivotal role in virus diagnosis.We have summarized several recent achievements and efforts in advancing bio-inspired imprinted polymers for virus identification in this work. The latest advancements demonstrate that the techniques for determining trace amounts, early diagnosis, and removal of viruses from imprinted polymers have evolved enormously. It obviously enhanced the understanding and knowledge of the production of various types of virus sensing and removal methods with sensors including quartz crystal microbalance, electrochemical, fluorescence, batch rebinding experiments, surface plasmon resonance methods, and so on. It should be noted that MIP-based methods, despite many associated challenges, have several important advantages that are sufficient to promote the growth of virus-determining strategies. Finally, there is a tremendous demand to develop the commercially diagnostic and point-of-care kits for virus detection and removal, which will ultimately lead to the realization and actual advancement in medicine and healthcare benefits. Only then, we will be able to enjoy their benefits in medical and other related areas.


Here we provide a granular, step-by-step calculation of the costs associated with publishing primary research articles, from submission, through peer-review, to publication, indexing and archiving. We find that these costs range from less than US$200 per article in modern, large scale publishing platforms using post-publication peer-review, to about US$1,000 per article in prestigious journals with rejection rates exceeding 90%. The publication costs for a representative scholarly article today come to lie at around US$400. These results appear uncontroversial as they not only match previous data using different methodologies, but also conform to the costs that many publishers have openly or privately shared. We discuss the numerous additional non-publication items that make up the difference between these publication costs and final price at the more expensive, legacy publishers.For decades, the supra-inflation increase of subscription prices for scholarly journals has concerned scholarly institutions. After years of fruitless efforts to solve this “serials crisis”, open access has been proposed as the latest potential solution. However, also the prices for open access publishing are high and are rising well beyond inflation. What has been missing from the public discussion so far is a quantitative approach to determine the actual The final per-article costs are then specified as a range depending on the number of articles published and the service level desired. These ranges denote current market rates at which customers can obtain publishing services.costs on average, it is necessary to arrive at the exact cost for each step in the processing workflow of a manuscript being submitted for publication. These direct or variable costs then have to be combined with the indirect or fixed costs of operating a publishing enterprise, such as staff costs, real estate, insurance and energy costs, etc. The former requires granular insight and expertise about the different service levels for the entire publishing workflow. The latter is commonly calculated as staff overhead. In this work, we have therefore calculated the cost for each step in the standard publication workflow under consideration of both fixed and variable costs. Both external and internal expenses have been taken into account as well as overhead costs to cover fixed non-direct company costs of the publishing venture.To arrive at a meaningful figure denoting how much the publication of an articleThere are three main areas in which production steps have to be considered: content acquisition, content preparation (production) and content dissemination/archiving. Importantly, ‘content acquisition’ does not imply active acquisition of authors and/or manuscripts.1.Content acquisitiona.Online submission systemb.Searching and assigning reviewersc.Communication with reviewersd.Communication with authorse.Handling of re-submission processf.Plagiarism checkg.Similarity Check (CrossRef)h.DOI for article (CrossRef)i.DOI for 2 or more reviews (CrossRef)j.APC collection2.Content preparation (production)a.Manuscript tracking systemb.Production system check-inc.Technical checking of manuscriptd.Copyeditinge.Typesettingf.Formatting figures/graphs/tablesg.Altmetric badgeh.XML and metadata preparationi.Handling author corrections3.Content dissemination/archivinga.Web OA platform and hostingb.Long-term digital preservation c.Distribution to indexing services Pricing figures have been deducted by openly available price lists of vendors, as for example for Scholastica, Akron Aps, CrossRef, CLOCKSS see,Table 2Expenses and fees for each individual service have been arrived at from two main sources. Some standard services have been taken from openly available price lists .. For services such as manuscript submission and peer review management systems we considered vendors such as Manuscript Central (Clarivate) and Editorial Manager (ARIES).Second, we requested quotes from vendors without publicly available fees, or turned to other sourcesOther costs such as internal staff costs  were estimated taking into account not only current market costs we have requested ourselves, but also numbers from major publishing houses . While some of these publishers have made their costs public , others For certain tasks, for example copyediting or typesetting, there are hundreds of individual companies worldwide providing those services on a industry-standard level. In our quote requests, we have considered only those with which we have collaborated in real business life so far or from which we know the performance and service level in detail from co-operations over two decades. Having compared the pricing of those service providers with others, we found only a very small variation of cost for such tasks, which justifies our practical approach. It was never our ambition to perform an exhaustive but always incomplete market study of service providers worldwide, but an attempt to provide an authoritative documentation of approximate current publishing costs as a valuable information tool for decision-makers and other stakeholders in policy drafting, contract negotiations or public discourse., with 1500 words on each page . (ii) We estimated an average STM article to contain 10 non-text items such as figures or tables. (iii) We also assumed an average rejection rate of 50% after conventional (pre-publication) peer-review with at least two reports and ten contact requests to secure one reviewer. (iv) We assume a desk-rejection rate of 10% after editorial review. (v) We also base our staff costs on the granular work load per article and not on full-time equivalents (FTE). These assumptions entail that all editorial duties (on average 7.5 person-hours per submitted manuscript) are handled by in-house staff and none by academic editors, while peer-review is still performed by volunteer academics. In this way, staff costs, including overhead expenses, are calculated on a per-article basis . Salary costs are based on industry standards in more economically developed countries for the different editorial tasks. Overhead expenses can vary significantly depending on the profit and loss structure of the publisher and include rent, repairs, depreciation, interest, insurance, travel expenditures, labor burden, telephone bills, supplies, taxes, accounting fees, etc. We have estimated an average 33% overhead on top of salary costs. The following publication tasks are commonly covered by annual (membership) fees plus an initial, one-time set-up or installment fee: Web OA platform and hosting, CLOCKSS/Portico, DOAJ, Altmetric Badge and Crossref. Because these costs accrue regardless of how many articles are published , we have calculated per-article costs for journals with different numbers of articles published per year. All of these assumptions have been made with the overarching goal to ensure upper-bound costs. For each of these cost items, there exist numerous ways in which their contributions to overall costs can be reduced. Thus, the figures we provide here describe an upper cost ceiling that many publishers will easily fall below.The calculation of per-article figures from costs that do not accrue on a per-article basis  was based on the following assumptions: (i) The average STM article contains 12 printed pagesWhile some general fixed costs are covered by salary overheads (see above), we deliberately chose to not include certain fixed costs: Cost of sales have not been considered because for open access journals no longer sales representatives are required which have to negotiate renewals of subscriptions with libraries on an annual basis. We also excluded management costs as these are highly variable and in large publishers with many journals (and hence articles), per article costs of management are often negligible. We realize that this may be different for publishers which publish low-volume journals but with nevertheless highly paid executives (see Discussion). Because making an article public  is distinct from locking it behind a paywall, we have also not calculated the often very significant paywall costs. While innovation (or acquisition of innovative technologies) as well as branding and advertising/marketing are crucial for a company to succeed and thrive in a market in the long term, we have also not included these costs as they are not directly related to publishing scholarly articles. Such costs would include conference attendance, advertisement in print, online, social media and search platforms, as well as search engine optimization (SEO). Similarly, government relations (lobbying) may be considered a necessary expense for any business, but as it does not directly relate to the process of publishing academic papers, we did not include these costs in our calculations either. However, we do discuss the probable extent to which these non-publication costs may affect pricing.The motivation for the above assumptions was to combine a robust cost calculation  with an upper bound cost calculation which would come to lie above most academic-run journals. However, the journal landscape is diverse and journals can be run on a shoestring budget, supported exclusively by volunteer labor and institutional resources, or by multi-billion dollar publicly traded corporations with professional in-house staff handling every individual step. In an attempt to reflect this heterogeneity, we divided our cost calculations into three broad categories, each with two sub-categories for a total of six scenarios .The first two scenarios A and B correspond to professionally run journals where salaried in-house staff handle each manuscript and only peer-reviewers provide volunteer labor. These correspond to traditional commercial journal publishing scenarios. Scenario A differs from Scenario B in that the individual production steps are not sourced from a variety of generic publishing service providers, each specializing in their particular publishing step, but from a full-service provider specialized in scholarly publishing, providing most of the publication services listed above, from a single source. In our example, we have chosen a service provider which is representative for this sector and with considerable name recognition, Scholastica, as such a specialized, full-service provider. Selecting a single, specialized provider is more convenient and requires less expertise than multiple generic providers, as a single contract replaces sourcing and contracting of multiple partners. However, such convenience commonly comes with an additional cost. Scenario A corresponds, e.g., to those society or university-run journals with salaried editors, while many corporate publishers run their journals according to Scenario B. The third scenario takes into account that many scholarly journals are operating with minimal budgets by not paying their editors at all, using institutional servers, for instance with the free, open source Open Journal System handling submission and peer-review, with little space for long-term preservation or indexing. Of course, their institution covers server costs for these journals, but with servers being shared and provided centrally already, per-article costs approach zero. This aspect is analogous to the salaries of the volunteer editors being paid for by their institutions, irrespective of how many hours of editorial work are being volunteered. At first approximation, Scenario A is likely to be the most expensive option, all else being equal, with Scenario B expected to come to lie between Scenario A and the least costly Scenario C.We calculated an additional sub-category for each scenario to better cover the scholarly diversity. For Scenario A and B we also considered an additional scenario where costs would be reduced by post-publication peer-review as it is practiced by journals like, e.g., F1000Research. In these scenarios, submitted manuscripts are published immediately and peer-review then merely creates additional versions, such that there are no more rejections after editorial review. Journals in Scenario C are often operated by individuals whose primary specialization is not scholarly publishing. Therefore, a provider that bundles the different publishing steps may be more expensive but enticing due to the convenience it offers. Therefore, we also calculated the costs for articles in such scholar-led journals, but with Scholastica replacing the generic service providers.All costs are calculated per published article, i.e., a journal that publishes 1,000 articles per year has received 2,000 articles if their rejection rate is 50%. Our costs are calculated for the 1,000 published articles, not for the 2,000 submissions the journal has received. For each of the six scenarios, we have also calculated the same costs, but assuming a 90% rejection rate (see raw data file). As fixed costs are distributed over all published articles, article volume per year is another factor we considered. Our calculations yielded a lower bound of 100 articles per year (see results), below which it becomes difficult to operate a journal with in-house staff. Beyond 1,000 articles per year, indirect costs per article shrink to a negligible fraction. We thus calculated per-article costs for each scenario for journals with 100 articles per year and for 1000 articles per year, for a grand total of 24 different cost estimates. The results for the 12 cases that represent the more common journals with an average rejection rate of 50% are depicted in, at the present time this is still a hypothetical scenario, despite repeated calls for such a platform since then. With such a modern, decentralized, federated platform providing publishing functionalities without journals .All the data we have based our calculations on are available at Figshare  or 1,000 articles (corresponding to 5 FTEs), to show the spread of fixed and indirect costs over the number of articles published.Our calculation of per-article publishing costs in a conventional pre-publication peer-review (50% rejection rate) scenario where all editorial duties are performed by in-house staff (Scenario B) ranges from US$643.61 for a journal that publishes 100 articles per year down to US$565.15 for such a journal that publishes 1,000 articles . These values consist of US$266.53 direct publishing costs , US$ 289.91 for editorial staff and US$8.72 to US$87.18 for 1,000 to 100 articles, respectively, in indirect costs .These numbers were calculated using generic, full-service providers (based in India), where applicable. There are open access service providers that provide packaged deals for the same services as these generic service providers. We have calculated the same steps using a well-known provider in this area, representative for this class of service providers, Scholastica (Scenario A). Not unexpectedly, these figures are slightly higher: US$ 374.08 for direct publishing costs and US$5.92 to US$59.18 for 1,000 to 100 articles, respectively, for indirect costs .While these costs have been calculated for a generic journal with 50% rejection rate, per-article costs will increase with increased rejection rates and decrease with less rejections as in, e.g., a post-publication peer-review (PPPR) model. In a journal that uses generic service providers and publishes all submitted manuscripts as PDF preprints with a DOI before performing otherwise identical peer-review as described above , per article editorial services drop from US$289.91 to US$140.69 (Scenario A2/B2), with all other costs remaining nearly identical. Conversely, prestigious journals with rejection rates of around 90% see their costs rise to US$1053.87 for 100 articles per year or US$770.53 for the larger journals with about 1,000 articles per year (generic service providers).These numbers also show that for a conventional journal today, where academics perform their editorial duties on a volunteer basis , direct publication costs come to lie at US$266.53 with generic service providers and total costs depend on the scale at which the journal operates. Small journals with 100 articles would face average per article total publication costs of US$353.71, while journals with 1,000 or more articles would only face costs of US$275.25 or less per published article. Even at the highest convenience for a small, volunteer-run journal, costs come to lie at US$454.63 where a full-service provider (Scholastica) handles all of the technical aspects of the work (Scenario C2).The above calculations . Such a platform would dispense with several production steps which are necessitated by the current balkanization of the literature in different journals published by different publishers, but keep others (see Methodology). In this scenario, the indirect and fixed costs per article approach zero due to the high number of published articles (but see Discussion), such that the only remaining costs would be the direct publishing costs of US$190.17 per published article.Because of the economies of scale and recent calls for the replacement of journals with a modern publishing platform, it becomes clear that publication costs only cover 15% of the subscription price  and comparing it to the low end of the average price estimate for a subscription article of about US$4,000n price . Assuminarticle .. In the last 30 years, this “serials crisis” has never been coherently addressed, let alone solved. With this work, we aim to provide more financial evidence for future evidence-based policies addressing the affordability problem of scholarly communication.Since the 1990s, it has been recognized that the prices of scholarly journals were escalating at unsustainable rates and we follow this precedent. Drawing from publicly available price lists and industry-standard service costs, we find that publishing costs per article vary from US$194.89 to US$723.16, depending on the level of service and publishing volume , when compared to an itemized sourcing of publishing services. In our cost calculation, we have not factored in the management cost of sourcing the itemized services, as we have not included company management in our calculations. Any decision between these two options will thus have to be made after factoring in such costs as well. and current APCs . SeeEven in the rare, most expensive case, these costs compare very favorably both to the current subscription pricing of around US$4,000-5,000, when the journal in all other aspects but article length follows our low-volume Scenario C2. Such numbers also highlight one of the problematic aspects of using per-article costs, averaged over a highly diverse publishing landscape.On the other end of the spectrum are small journals that are run mainly on volunteer efforts. Even in cases where these journals use specialized full-service providers such as Scholastica, there are numerous ways to reduce per-article costs to below the US$100 mark. For instance, specializing in rapid dissemination of short articles reduces per-article costs at the Journal “Findings” to below US$100. Our calculations also fall in the same range as other methodologies.The workflow we model consists of verifiable, modular components, available to any entity with the desire to enter the academic publishing world. Numerous publishers are already on the record to operate at similar costs to the ones we have calculated. These publishers include, but are not limited to SciELO, Pensoft/arpha, Open Library of the Humanities, Ubiquity, PeerJ or Scholastica. Our data confirm that at prices of around US$500 per article, these providers stand to arrive at around a 10% profit margin. Further corroborating these calculations, the 2018 STM report cites survey-based data that arrive at only slightly higher average costs than our calculation . These insights are important for designing a transition towards a scholarly publishing platform instead of journals.Our calculations also show that with publishing volumes exceeding 1,000 articles per year, fixed costs shrink below 1% of the direct article costs and become negligible. This was expected and already concluded in a previous analysisDue to the limited possibility in dividing labor contracts into arbitrarily small portions, we find that journals with volumes below approx. 100 articles per year would be best served financially if they operated on the concept of volunteer academic editors handling the peer-review, instead of in-house staff.In conclusion, given the congruence of the available data and the publicly available prices for the services required, the market rate ranges for publication services we arrive at here do not appear controversial. Perhaps more controversial is the number and amount of non-publication costs a scholarly article, funded by the taxpayer, ought to accrue. and generous publication costs of US$600 per article , a conservative 30% profit margin  for one of the large publishersRunning a business: Management. While our cost calculations include generic running costs such as rent, repairs, depreciation, interest, insurance, travel expenditures, labor burden, telephone bills, supplies, taxes, accounting fees, etc., we have explicitly omitted some indirect costs such as management cost and paywalls. For instance, according to their 2016 tax statement, the New England Journal of Medicine spends 4% of its publication revenue on their top ten management staff alone .. These costs accrue by seeking to enclose the scholarly literature within the paywalls of publishers via alternative routes in addition to the digital paywalls.On top of the technical costs of a paywall, one may also consider the legal fees for defending paywalls for this cost item. Publishers have a track record of litigation with regard to articles outside of their paywalls and regularly seek damages in court for actual or perceived threats to their subscription business modelNews, advertising, sales, marketing, public relations: branding. Another cost item is publishing non-research content. For instance, for 2017, PubMed lists a total of 1,595 articles published by the Lancet, while Clarivate Analytics only counts 302 articles for their Impact Factor. Assuming that only the latter articles amount to primary research publications, this journal’s revenue also pays for 1,293 non-research articles. Similar numbers also hold for other prestigious journals , often with their own journalist and editorial staff commissioning articles and/or reporting themselves on research and policy news. However, the number of journals where this can constitute a significant fraction of their total costs is presumably small, likely restricted to the most prestigious journals.Prestigious journals also often practice active author or materials acquisition, by traveling to conferences and laboratories, building networks in a strategy to entice the next exciting research finding to be published in their journals. Active author acquisition accrues costs both in terms of travel and time spent networking and communicating with authors that is not covered in our cost calculations (see Methods).Sometimes, new journals also need to engage in such author acquisition practices, which, perhaps, can be best subsumed under general marketing or public relations costs required for building and maintaining a brand. These marketing costs also include, e.g., advertising in various venues targeting both authors and subscribers. For many publishers it is also common to promote their brand at conferences and institutions with, e.g., hosted speakers, travel grants or sponsored awards.Because of the complex, time-consuming negotiations with libraries on ever tighter budgets due to the supra-inflationary subscription price increases, publishers also need to employ expert sales teams. The task of these sales teams is not only to find the most irresistible way to package and bundle subscription journals and/or databases, but also to device the most inexorable psychological strategy for their negotiations with librarians. These sales teams need to operate in close connections with the various advertising, marketing and public relations teams of the publisher to accomplish a coherent brand image. One may argue that in times of OA, these sales costs are not necessary expenses any more and more associated with paywall costs than with publication costs. On the other hand, in an OA world, one may argue that branding was never more important for author acquisition.New technologies: innovation and acquisitions. Publishers also need to invest in innovation, in order to stay current with their technologies and functionalities. While scholarly publishers have been quick to transition from print to web-based technologies in the past, the digital functionalities of most of the scholarly literature today lag at least a decade behind current functionalities of other digital objects outside of the scholarly literature. The level of investment in innovation thus remains unclear and its effects questionable. Instead of investments into their own technological innovation, publishers today appear to acquire companies that have invented desired functionalities around the scholarly workflow, with the goal to provide services beyond publications.Government relations: Lobbying. Most international publishers, as any other corporation, also spend significant amounts of money on government relations . Some of these corporations employ staff at the vice president level not only in the most important research nations, but also at the level of supra-national bodies such as the European Commission. These staff, in turn, employ assistants and other members of their teams. Obviously, the task of these employees is to protect current revenue streams, e.g., subscription or APC income. For instance, one publisher, Elsevier, spends more than 400,000€ per year on lobbying at the level of the European Commission alone. The consequences of such efforts have been observable, e.g., in the so-called “Finch Report” in the UK, which surprised many commentators with its publisher-friendly recommendations .Data are available under the terms of the All initial concerns and recommendations were addressed in the revised version of the manuscript.Is the work clearly and accurately presented and does it cite the current literature?PartlyIf applicable, is the statistical analysis and its interpretation appropriate?Not applicableAre all the source data underlying the results available to ensure full reproducibility?YesIs the study design appropriate and is the work technically sound?YesAre the conclusions drawn adequately supported by the results?YesAre sufficient details of methods and analysis provided to allow replication by others?YesReviewer Expertise:Scholarly communication, Open peer reviewI confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Is the work clearly and accurately presented and does it cite the current literature?PartlyIf applicable, is the statistical analysis and its interpretation appropriate?Not applicableAre all the source data underlying the results available to ensure full reproducibility?PartlyIs the study design appropriate and is the work technically sound?YesAre the conclusions drawn adequately supported by the results?YesAre sufficient details of methods and analysis provided to allow replication by others?YesReviewer Expertise:Library science, information literacy, citation analyses, circulation and journal/book pricing analyses.I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. I concur that the “supra-inflation increase of subscription prices for scholarly journals” is a critical issue, especially for academic libraries, and that this is a valuable contribution to the literature. I also concur with the previous reviewer that the “scenarios” and tables could be better explained and organized for greater clarity. Also further indicators of variance would be helpful - for example, there are surely significant differences  based on geographic location. I also find myself wondering which (if any) of the costs to publishers are tax deductible, which would effectively increase the profit margin.cost of producing articles, to place this in broader perspective It would be helpful to clarify more explicitly that there are two majorprice components to journal articles: (1) Journal subscription costs, which are typically borne by libraries , and (2) article-processing charges (APC’s) which are in principle an open-access alternative to subscriptions, but in practice often simply shift the cost from an institution’s library to its faculty, research office and/or some other institutionally-funded entity. Both contribute directly or indirectly to the high price of student tuition and the chronic under-funding of many academic libraries, but subscription prices seem to be the greater issue since the average “per article price” (see below) is considerably higher.  While the main focus of the manuscript is the For readers not necessarily familiar with the various journal pricing models, the authors might note that both journal prices and APC’s vary enormously by discipline, especially STEM vs. humanities, and that the practice of “Big Deal” bundling  can make it very difficult for librarians to disentangle the actual subscription cost per journal. It would be helpful to include some discussion and more explicit data on the widely varying range of APC’s, which, in my experience, seem independent of actual subscription costs. I am more familiar with the pricing models for STEM journals , but it is my impression that when humanities journals do charge authors, the fee is much lower. This would be an interesting topic to explore in a follow-up article. Granted that STEM articles typically include multiple tables and figures that are costly to produce, but is the price differential really as substantial as the differences in subscription costs or APC’s? In the final paragraph of the results (p.6) and in Figure 1, the authors compare the article cost with “the average price estimate for a subscription article of about US$4,000”. Where did this figure come from and what is it based on? Is this an across the board “per library” average, in which case the wide variation in prices paid by different libraries (at least in the US) is surely another confounding factor. Again, there should be some discussion of the vast difference in pricing among disciplines, or if this is based on STEM journals as I suspect, that should be clarified. Also the average APC price should be included in the comparison; it is interesting that it appears to be considerably less than the quoted US$4,000 subscription “per article” cost. This brings up a further question for the future: in hybrid journals, does charging APC’s result in lower subscription prices, or are APC’s effectively layered on top of subscription prices? Another point that is only tangentially referenced (e.g. “volunteer academic editors”) is that many of the costs associated with publishing are actually borne by the institution and its academic faculty, who not only produce the scholarship but also review articles and often act as editors as well. This labor is typically unpaid. “Volunteer academic editors” in well-funded institutions may receive some form of course release, additional office space and/or clerical support, but again (see first paragraph) these costs are borne by the institution and to some degree passed on to its students; they are not borne by the publishers. Of course this point has been made many times before, but since the authors are discussing various costs involved in publication it is worth noting again. As a final comment, it would be informative to have responses from publishers, especially small “non-profit” or “not-for-profit” publishers on this publication. Very thought provoking!Is the work clearly and accurately presented and does it cite the current literature?PartlyIf applicable, is the statistical analysis and its interpretation appropriate?Not applicableAre all the source data underlying the results available to ensure full reproducibility?PartlyIs the study design appropriate and is the work technically sound?YesAre the conclusions drawn adequately supported by the results?YesAre sufficient details of methods and analysis provided to allow replication by others?YesReviewer Expertise:Library science, information literacy, citation analyses, circulation and journal/book pricing analyses.I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Response to Reviewer #2: Lisa Rose-Wiles:I also concur with the previous reviewer that the “scenarios” and tables could be better explained and organized for greater clarity.We thank both reviewers for their suggestions and are confident to have now adequately addressed this very valid concern in the new, revised version of the manuscript.Also further indicators of variance would be helpful - for example, there are surely significant differences  based on geographic location. I also find myself wondering which (if any) of the costs to publishers are tax deductible, which would effectively increase the profit margin.We have now further emphasized that our salary calculations are based on western  industry standards and that countries with lower salary levels would hence face lower costs. This is to arrive at upper bound figures, describing the costliest way of publishing, from which one can always find ways to reduce costs. We have further emphasized this approach also at the very beginning of the Discussion section now.While the main focus of the manuscript is the cost of producing articles, to place this in broader perspective It would be helpful to clarify more explicitly that there are two major price components to journal articles: (1) Journal subscription costs, which are typically borne by libraries , and (2) article-processing charges (APC's) which are in principle an open-access alternative to subscriptions, but in practice often simply shift the cost from an institution's library to its faculty, research office and/or some other institutionally-funded entity. Both contribute directly or indirectly to the high price of student tuition and the chronic under-funding of many academic libraries, but subscription prices seem to be the greater issue since the average “per article price” (see below) is considerably higher.For readers not necessarily familiar with the various journal pricing models, the authors might note that both journal prices and APC's vary enormously by discipline, especially STEM vs. humanities, and that the practice of “Big Deal” bundling  can make it very difficult for librarians to disentangle the actual subscription cost per journal. It would be helpful to include some discussion and more explicit data on the widely varying range of APC's, which, in my experience, seem independent of actual subscription costs. I am more familiar with the pricing models for STEM journals , but it is my impression that when humanities journals do charge authors, the fee is much lower. This would be an interesting topic to explore in a follow-up article. Granted that STEM articles typically include multiple tables and figures that are costly to produce, but is the price differential really as substantial as the differences in subscription costs or APC's?We agree with all the arguments here. Therefore, we now more explicitly reference the longer, preprint version of our manuscript, where we not only discuss pricing strategies and business models, as suggested, but also policy options. However, in this more condensed version, we made a conscious effort to focus exclusively on the cost aspect, as we felt the original version was too long, unwieldy and difficult to read as it was covering too many topics at the same time.In the final paragraph of the results (p.6) and in Figure 1, the authors compare the article cost with “the average price estimate for a subscription article of about US$4,000”. Where did this figure come from and what is it based on? Is this an across the board “per library” average, in which case the wide variation in prices paid by different libraries (at least in the US) is surely another confounding factor.This explanation was indeed lost as we transitioned from our longer preprint version to this shorter one. We are very grateful for having this pointed out. We now reference the sources of these calculations. The most recent one is very simple: dividing the estimated US$10b in journal revenue by the number of published articles (2m): ~5k. As some other sources mention 4k, we went with the lower bound of these estimates in the literature.Again, there should be some discussion of the vast difference in pricing among disciplines, or if this is based on STEM journals as I suspect, that should be clarified. Also the average APC price should be included in the comparison; it is interesting that it appears to be considerably less than the quoted US$4,000 subscription “per article” cost. This brings up a further question for the future: in hybrid journals, does charging APC's result in lower subscription prices, or are APC's effectively layered on top of subscription prices?We now mention the APC price range of US$1,400-2,200 and the 8 references upon which we base this range.Another point that is only tangentially referenced (e.g. “volunteer academic editors”) is that many of the costs associated with publishing are actually borne by the institution and its academic faculty, who not only produce the scholarship but also review articles and often act as editors as well. This labor is typically unpaid. “Volunteer academic editors” in well-funded institutions may receive some form of course release, additional office space and/or clerical support, but again (see first paragraph) these costs are borne by the institution and to some degree passed on to its students; they are not borne by the publishers. Of course this point has been made many times before, but since the authors are discussing various costs involved in publication it is worth noting again.We now make it more explicit what is being paid in terms of salary and which work is being carried out by volunteers. We also explicitly mention the costs covered by institutions  and relate them to per-article cost.As a final comment, it would be informative to have responses from publishers, especially small “non-profit” or “not-for-profit” publishers on this publication.We list numerous publishers which are already on the record for publishing in this cost range and cite journals that have much lower costs than our figures. In the acknowledgements, we mention that we have been made privy of internal cost structures to validate and test our figures. As we mention in the article, our numbers match those from other methodologies (e.g. surveys). The preprint version has been available since 2019 and has even received attention in trade organs such as the “Scholarly Kitchen”. In other words, publishers have already vetted our numbers and have had ample opportunity over a number of years to comment on our work and improve it by criticism. Given that our numbers match so well with the available evidence and that our article has received considerable attention from the industry since 2019, perhaps one may interpret the fact that the expensive legacy publishers so far have not publicly commented on these numbers, as evidence that there may not be much left to criticize? Of course, another reason may be that the more expensive publishers may hesitate to draw more attention to the fact that they are so much more expensive. In this case, we would appreciate any suggestions in how we may be able to force these publishers to acknowledge and comment on our calculations. F1000Research allows for comments on the manuscript and perhaps a drive to invite publishers of all ranges to contribute so such a comment may be instructive? Society publishers, so far, have refrained from public comments other than generally stating that they use publication income to finance society services. We allude to many such and related costs in the “non-publication costs” section of the manuscript. This article reports a breakdown of article publication costs —from manuscript submission to indexing— for different publication scenarios. There are at least two fundamental reasons why analysing and reporting the realistic cost of publishing a research article is of paramount importance. First, given the exorbitant sums of public money spent to publish the world’s scholarly output it is imperative that we know where exactly this money goes. This information can perhaps mobilise governments, funders, individual scholars, and the general public to demand more sustainable publication models that provide only those essential services that truly add value to scholarly works. Second, a granular account of publishing costs can incentivise more scientific societies and academic groups to abandon their commercial publishers and establish alternative models that better serve the needs of scholarly communication. There is no doubt therefore that this is an extremely valuable report that should be widely disseminated. My review will mainly focus on some recommendations that in my opinion would improve the presentation and utility of the results. The cost analysis provided in this report is based on a list of 24 services grouped in three distinct categories: content acquisition, preparation, and dissemination. A first minor observation is that in the category of content acquisition, it would probably be more intuitive to list “online submission system” as the first item (before “searching and assigning reviewers”) to match the publication workflow. A second and more important observation is that in this list, and throughout the manuscript, services are sometimes confounded with service providers. Since there are more than one providers for each of the services, I strongly recommend that the list only includes services, whereas in the manuscript different options for each service can be discussed. For example Crossref is not the only option for “DOI registration”, which I believe should be the title of this particular service. Similarly, the service provided by CLOCKSS/LOCKSS/Portico, could be called “long-term digital preservation”. Also, it is not clear what the service provided by OAPEN is, while “upload to Scopus…”, could be called “distribution to indexing services”. Should the authors decide to follow this recommendation I would advise to also modify the accompanying excel file accordingly. The “Direct or variable costs” subsection in the methods section would be easier to follow if it was structured differently, starting with the list of services and then explaining how pricing information was obtained. Following the logic that the list of services is the nucleus of the cost analysis, and the report itself, I suggest that table 1 is modified so that the first column displays the services and the second column the providers. Also, it is important that the terms in the services list are used consistently throughout the manuscript. For example, in table 1 we find a service termed “peer review” and another called “peer review management”. It is not clear how these services correspond to the original list. When a service provider offers more than one service in the list, I would recommend to include all of these services in the table. If it is considered convenient to create a new grouping , it should be clear —in the table and in the manuscript— which services from the original list are included in this group . The “scenarios” section should include a more thorough description of the different scenarios, as well as the motivation for selecting each of these scenarios as a separate use case. This description of what each scenario refers to is attempted in the “results” section but in a rather anarchic and hard to follow manner. In the “scenarios” section the authors vaguely mention that these scenarios “...correspond either to existing publishing options or to options that have been discussed in the literature”, but neither are these options clearly delimited nor specific references are provided. I therefore found it very hard by reading the manuscript to understand exactly which publication model, combination of services, and choice of providers each scenario refers to. This was made possible only by carefully analysing the formulas for the different calculations in the excel file. However, even after this more careful analysis, the motivation behind each scenario remained unclear. For example, it seems that the only difference between scenarios A and B in terms of content acquisition is using one service provider instead of another. In scenario A scholastica is used for online submission management (cell L18), while Akron is used in scenario B (cell J19). I recommend that the different scenarios are not defined based on the choice of specific providers but according to different, clearly explained publication models, characterised, for example, by use of existing publishing infrastructure , variable rejection rates, number of published articles, review policies, voluntary or hired editorial work, etc. The available choice of providers for specific services (or groups of services) and their impact on the costs can be discussed in the manuscript and even presented as a separate table. However, I consider it important that the initial scenarios are reported without any reference to specific providers but rather using average (or low/high) estimates. Otherwise, in their present form, tables 3 and 4 are very hard to follow. In both tables publication choices  are mixed with providers  without a clear description (in the table or the manuscript) of the different publication models, or the services offered by each provider. For example, from the excel file I deduced that scenarios A2, B2 and C do not include costs for online submission, but it is not clear from the discussion in the manuscript or from the brief labels in table 3, which exact models allow the omission of these costs and how. Insisting on the necessity to adequately describe the different publication scenarios, in the “scenarios” section the authors refer to a “decentralized/federated platform providing publishing functionalities”. However, again it is not clear what are the foundations of this model , and whether this model is represented in one of the scenarios. Similarly, the authors briefly mention a PPPR model in the “results” section but there is no clear description of what exactly this model entails and which services from the original list allows to omit or circumvent. To summarise, I strongly recommend that the different publication scenarios refer to publication options (not choice of providers) and that they are concisely described in the corresponding section with references to the literature or to existing examples when possible. It should be clear which services from the list correspond to each scenario and how different scenarios allow the omission of certain services. The different options for service providers should be discussed separately. For example, it would be useful to report the impact on the publication costs of choosing scholastica or Akron as a provider for a specific list of services  in a given publication scenario. As a minor comment, I suspect that J21 is missing from the formula used to calculate cell J26. I would recommend that the authors had another careful look at their formulas to avoid similar omissions or errors. Overall, I commend the authors for their work and invite them to consider my recommendations that I believe will significantly improve the uptake of this extremely valuable information. References: [1] https://www.coar-repositories.org/news-updates/what-we-do/next-generation-repositories/Is the work clearly and accurately presented and does it cite the current literature?PartlyIf applicable, is the statistical analysis and its interpretation appropriate?Not applicableAre all the source data underlying the results available to ensure full reproducibility?YesIs the study design appropriate and is the work technically sound?YesAre the conclusions drawn adequately supported by the results?YesAre sufficient details of methods and analysis provided to allow replication by others?YesReviewer Expertise:Scholarly communication, Open peer reviewI confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Response to Reviewer #1: Pandelis Perakakis:The cost analysis provided in this report is based on a list of 24 services grouped in three distinct categories: content acquisition, preparation, and dissemination. A first minor observation is that in the category of content acquisition, it would probably be more intuitive to list “online submission system” as the first item (before “searching and assigning reviewers”) to match the publication workflow.Thank you, corrected.A second and more important observation is that in this list, and throughout the manuscript, services are sometimes confounded with service providers. Since there are more than one providers for each of the services, I strongly recommend that the list only includes services, whereas in the manuscript different options for each service can be discussed. For example Crossref is not the only option for “DOI registration”, which I believe should be the title of this particular service. Similarly, the service provided by CLOCKSS/LOCKSS/Portico, could be called “long-term digital preservation”. Also, it is not clear what the service provided by OAPEN is, while “upload to Scopus…”, could be called “distribution to indexing services”. Should the authors decide to follow this recommendation I would advise to also modify the accompanying excel file accordingly.This was our oversight and it is an excellent suggestion. We are now following it 100%, also in the Excel spreadsheet.The “Direct or variable costs” subsection in the methods section would be easier to follow if it was structured differently, starting with the list of services and then explaining how pricing information was obtained.This is how it should be and we have no good explanation for why we did not write it that way. We have now re-ordered all components as suggested.Following the logic that the list of services is the nucleus of the cost analysis, and the report itself, I suggest that table 1 is modified so that the first column displays the services and the second column the providers.Corrected.Also, it is important that the terms in the services list are used consistently throughout the manuscript. For example, in table 1 we find a service termed “peer review” and another called “peer review management”. It is not clear how these services correspond to the original list. When a service provider offers more than one service in the list, I would recommend to include all of these services in the table. If it is considered convenient to create a new grouping , it should be clear -in the table and in the manuscript- which services from the original list are included in this group .I see the point here, of course. We have been able to quickly fix the instances where it was just a matter of replacing a few words. However, it was not easy to address this very relevant point everywhere, as it is many times easier to refer to a series of steps with a shorthand rather than with a long list. Sometimes that shorthand can be a provider , sometimes it is a functionality such as, e.g., “OJS” for a system that manages submission, manuscript tracking and review management all at the same time. We have tried to rephrase as many of such instances as possible, but we are not sure if we were able to address this point in every single instance.The “scenarios” section should include a more thorough description of the different scenarios, as well as the motivation for selecting each of these scenarios as a separate use case. This description of what each scenario refers to is attempted in the “results” section but in a rather anarchic and hard to follow manner. In the “scenarios” section the authors vaguely mention that these scenarios “...correspond either to existing publishing options or to options that have been discussed in the literature”, but neither are these options clearly delimited nor specific references are provided. I therefore found it very hard by reading the manuscript to understand exactly which publication model, combination of services, and choice of providers each scenario refers to. This was made possible only by carefully analysing the formulas for the different calculations in the excel file. However, even after this more careful analysis, the motivation behind each scenario remained unclear. For example, it seems that the only difference between scenarios A and B in terms of content acquisition is using one service provider instead of another. In scenario A scholastica is used for online submission management (cell L18), while Akron is used in scenario B (cell J19).I recommend that the different scenarios are not defined based on the choice of specific providers but according to different, clearly explained publication models, characterised, for example, by use of existing publishing infrastructure , variable rejection rates, number of published articles, review policies, voluntary or hired editorial work, etc. The available choice of providers for specific services (or groups of services) and their impact on the costs can be discussed in the manuscript and even presented as a separate table. However, I consider it important that the initial scenarios are reported without any reference to specific providers but rather using average (or low/high) estimates. Otherwise, in their present form, tables 3 and 4 are very hard to follow. In both tables publication choices  are mixed with providers  without a clear description (in the table or the manuscript) of the different publication models, or the services offered by each provider. For example, from the excel file I deduced that scenarios A2, B2 and C do not include costs for online submission, but it is not clear from the discussion in the manuscript or from the brief labels in table 3, which exact models allow the omission of these costs and how.It is completely obvious how this section must be confusing for readers and, again, we do not have a good explanation for why we did not provide sufficient detail. Our lack of explanation could also be seen in some of Lisa Rose-Wiles’ comments. In attempting to follow these suggestions, we now have provided not only detailed explanations for each scenario in the text, but have also updated Table 3. In brief, scenario A and B differ in that B cases source multiple, generic publishing providers for the different steps , while A sources many steps from a single provider, specialized in scholarly publishing . Scenario C also covers all steps in principle, but does not count some costs such as editors (volunteers) or servers  or a submission/tracking system . Post-publication peer-review decreases rejections and hence price (A2/B2). Scenario C2 replaces, e.g., servers and OJS with Scholastica.Insisting on the necessity to adequately describe the different publication scenarios, in the “scenarios” section the authors refer to a “decentralized/federated platform providing publishing functionalities”. However, again it is not clear what are the foundations of this model , and whether this model is represented in one of the scenarios. Similarly, the authors briefly mention a PPPR model in the “results” section but there is no clear description of what exactly this model entails and which services from the original list allows to omit or circumvent.We now cite Perakakis et al. 2010 very prominently, as well as the COAR report, together with a brief explanation of the concept. Both are referenced with the name they gave these solutions, i.e., “global open archive” or ”next generation repository”, respectively.To summarise, I strongly recommend that the different publication scenarios refer to publication options (not choice of providers) and that they are concisely described in the corresponding section with references to the literature or to existing examples when possible. It should be clear which services from the list correspond to each scenario and how different scenarios allow the omission of certain services. The different options for service providers should be discussed separately. For example, it would be useful to report the impact on the publication costs of choosing scholastica or Akron as a provider for a specific list of services  in a given publication scenario.We are confident that the current version now addresses all the raised issues and that our choice of scenarios becomes clearer in the way we explain them now.As a minor comment, I suspect that J21 is missing from the formula used to calculate cell J26. I would recommend that the authors had another careful look at their formulas to avoid similar omissions or errors.We have triple-checked these cells in the spreadsheet and could not find any missing values. We have also checked all adjacent cells for possible errors and were not able to find any. We have gone over the entire spreadsheet both for the consistency of the calculations, the accuracy of the text descriptions and whether any of the costs needed to be updated due to change market rates. We have not been able to locate any problems. We suggest arranging an online call with video and screen sharing to identify and remove potential errors we may have missed or are unable to identify.


Varroa destructor leads to fatal or symptomatic infections of individuals, usually followed by collapse of the entire colony.Deformed wing virus (DWV) is a bee-pathogenic, originally rather benign, single- and positive-stranded RNA virus. Only the vectorial transmission of this virus to honey bees by the ectoparasitic mite  Varroa destructor. Symptoms of overt infections are pupal death, bees emerging with deformed wings and shortened abdomens, or cognitive impairment due to brain infection. So far, three variants of DWV, DWV-A, DWV-B, and DWV-C, have been described. While it is widely accepted that V. destructor acts as vector of DWV, the question of whether the mite only functions as a mechanical vector or whether DWV can infect the mite, thus using it as a biological vector, is hotly debated because in the literature data can be found that support both hypotheses. In order to settle this scientific dispute, we analyzed putatively DWV-infected mites with a newly established protocol for fluorescence in situ hybridization of mites and demonstrated DWV-specific signals inside mite cells. We provide compelling and direct evidence that DWV-B infects the intestinal epithelium and the salivary glands of V. destructor. In contrast, no evidence for DWV-A infecting mite cells was found. Our data are key to understanding the pathobiology of DWV, the mite’s role as a biological DWV vector, and the quasispecies dynamics of this RNA virus when switching between insect and arachnid host species.Deformed wing virus (DWV) is a bee-pathogenic, single- and positive-stranded RNA virus that has been involved in severe honey bee colony losses worldwide. DWV, when transmitted horizontally or vertically from bee to bee, causes mainly covert infections not associated with any visible symptoms or damage. Overt infections occur after vectorial transmission of DWV to the developing bee pupae through the ectoparasitic mite IMPORTANCE Deformed wing virus (DWV) is a bee-pathogenic, originally rather benign, single- and positive-stranded RNA virus. Only the vectorial transmission of this virus to honey bees by the ectoparasitic mite Varroa destructor leads to fatal or symptomatic infections of individuals, usually followed by collapse of the entire colony. Studies on whether the mite only acts as a mechanical virus vector or whether DWV can infect the mite and thus use it as a biological vector have led to disparate results. In our study using fluorescence in situ hybridization, we provide compelling and direct evidence that at least the DWV-B variant infects the gut epithelium and the salivary glands of V. destructor. Hence, the host range of DWV includes both bees (Insecta) and mites (Arachnida). Our data contribute to a better understanding of the triangular relationship between honey bees, V. destructor, and DWV and the evolution of virulence in this viral bee pathogen. Apis mellifera) is a generalist, prolific, and versatile pollinator that is also quite easy to manage. Honey bees are therefore the most widely used commercial pollinator in agriculture and thus make a significant contribution to global crop production. Unfortunately, the health and well-being of honey bees around the world is threatened by a wide variety of pathogens and parasites. Viruses, especially those transmitted by the ectoparasitic mite Varroa destructor, play a major role in the worldwide reported losses of honey bee colonies. The virus, which is most often implicated in mite-related colony losses, is deformed wing virus (DWV) and is considered the most important reemerging pathogen of honey bees  because it was isolated as virus replicating in the mite  analysis protocol for mites in order to be able to detect DWV directly inside mite cells as visual proof of infection. Using this protocol, we analyzed mites that were DWV infected according to prior RT-PCR analysis to see if we could, in fact, provide the missing direct evidence for DWV infection in mites and identify mite tissues targeted by DWV.Whether or not DWV or certain variants of this virus can replicate in mites is crucial for understanding the pathogenesis of DWV infections and the relationship between a colony , 20, 25.V. destructor mites, we selected six mite- and virus-free colonies at the beginning of the bee season, which were managed throughout the season without any treatment against V. destructor to allow the undisturbed development of the mite populations and evolution of DWV quasispecies in these colonies. In late August, when the first crippled bees appeared in these colonies, we determined the mite infestation rate by counting the natural mite dead fall over 7 days (21 to 28 August). The six colonies split into three significantly different groups  exhibiting low (<100 mites), medium (330 to 600 mites), and high  infestation rates (P = 0.146) between the six colonies; 83.3% to 100% of the analyzed mites tested positive via RT-PCR for the DWV-positive strand (P = 0.005) between the colonies with respect to the proportion of DWV-infected mites (3 × 10 mites collected from the bottom board), i.e., which tested positive for the replicative negative strand of DWV via tagged strand-specific RT-PCR (P ≤ 0.008) proportion of crippled bees  than the proportion of crippled bees in the two colonies which had a low mite infestation level and a low rate of infected mites  stains and fluorescence in situ hybridization (FISH) analyses using V. destructor-specific probes. In H&E-stained cross sections of adult mites, brain, salivary glands, individual muscle bundles, ventriculus, lower gastric cecum, and upper gastric cecum were easily identified  variants evolved when DWV, an insect virus, was confronted with a new potential host, the mite V. destructor, and expanded its host range to include this arachnid. Every switch from the insect to the arachnid host and back again presumably represents an evolutionary bottleneck for the infecting DWV mutant clouds resulting in the selection of DWV-B- or DWV-A-like founder viruses adapted to replication in mites or bees, respectively. Error-prone replication of these founder viruses in the mite or bee host will again generate a mutant cloud that contains mutants capable of switching the host again. In order to fully understand how DWV manages to move between the honey bee and the mite host, we need to identify the relevant DWV genome sequence and protein signatures, which determine host specificity and tissue tropism. We propose that the presence of these molecular signatures regardless of the overall genomic context (DWV-A- or DWV-B-like) determines host specificity and virulence and that detecting these signatures will allow a much better assessment of DWV host specificity and virulence than the overly general classification into the known DWV variants.Based on our previous results , 20, 25 A. mellifera colonies of the Institute for Bee Research in Hohen Neuendorf, Germany. Mid-March 2019, at the beginning of the honey bee season, 16 honey bee colonies that did not show any signs of overt DWV infections (crippled bees) were screened for DWV, sacbrood virus (SBV), chronic bee paralysis virus (CBPV), and Kashmir bee virus (KBV) infections by molecular diagnostics. To this end, larvae, pupae, and adult worker bees  were sampled from each colony, and virus diagnostic was performed as previously described , the middle (n = 10), and the lower right (n = 10) area of the boards, were sampled individually in 1.5-ml reaction tubes (Eppendorf), and the proportion of DWV-positive and DWV-infected mites was analyzed. To this end, extraction of total RNA from V. destructor mites as well as qualitative one-step RT-PCR analysis for the detection of the DWV-positive strand (mites positive for DWV)   and qualfor DWV)  were perfor DWV) , 25, 45.The proportion of crippled bees  was alsoin situ hybridization (FISH). Several samples of 50 to 100 adult worker bees were collected in 50-ml Falcon tubes , and bees were immobilized on ice for 10 min. Phoretic mites were removed from the bees with forceps and individually transferred into 1.5-ml reaction tubes (Eppendorf) for fixation with 1.0 ml of 4% Roti Histofix  for 2 h at room temperature (RT). Subsequently, the mites were washed with 1.0 ml of 6.8% sucrose in phosphate-buffered saline (PBS) (pH 7.0) overnight at RT, followed by a dehydration step with 100% acetone for 8 h at RT with gentle agitation on a shaker. The mites were preinfiltrated with 1.0 ml of 50% acetone/50% Technovit 7100  overnight at RT and subsequently infiltrated with 1.0 ml Technovit 7100 infiltration solution supplemented with 1% hardener I (wt/vol) for 24 h at RT with gentle agitation. Next, the mites were incubated in 500 µl of 14% sodium hypochloride  for 60 min with gentle agitation followed by three washing steps with Technovit 7100 infiltration solution. For embedding, infiltrated mites were carefully placed in precooled (−20°C) histoforms. The histoform wells were filled with 1.0 ml Technovit 7100 resin (infiltration solution supplemented with 6.66% [vol/vol] hardener II) and were incubated overnight at 4°C to allow gentle polymerization. Next, the embedded tissue was blocked with Technovit 3040 resin according to the manufacturer’s protocol. Histological semithin sections (8 to 10 µm) were prepared by using a rotary microtome  and a tungsten carbide knife with a D profile . All native histological sections were fixed on glass slides with tap water and stored at 4°C until further processing.Colony no. 118 harboring a mite population with a high proportion of DWV-infected mites , was used as the source colony for mites to be analyzed with fluorescence Native mite sections were stained with the modified hematoxylin-eosin (H&E) fast staining kit  according to the manufacturer’s protocol. Briefly, sections were stained with H&E solution 1 for 6 min and rinsed with tap water for 10 s. Subsequently, the tissue was covered with 0.1% hydrochloric acid, and after incubation for 10 s, the slide was rinsed with tap water for 6 min. H&E solution 2 was added to the slides and was removed after 30 s by rinsing with tap water for another 30 s. Stained mite sections were air dried and covered with a cover slip by using Entellan .NC_004830.2 and NC_006494.1). All virus-specific oligonucleotides represent antisense probes, which hybridize to the positive strand of the DWV-A or DWV-B genomes. A 5′-TexasRed-labeled nonsense oligonucleotide (nonsense)  oligonucleotides  as probes for the specific detection of DWV-A or DWV-B RNA ; Fig. 3.onsense)  was usedV. destructor-specific oligonucleotides were used. The oligonucleotides Vd-P1 and Vd-P2 .To visualize the cytoplasm of the mite cells, 5′-FITC (fluorescein isothiocyanate)-labeled, nd Vd-P2  were desFor hybridization, mite sections were washed three times with 1× PBS  in diethyl pyrocarbonate (DEPC)-treated water. To improve permeability of the mite sections, incubation with proteinase K (1 µg/ml) in 1× PBS for 10 min at 37°C was performed prior to hybridization. FISH was performed in Corning hybridization chambers  with LifterSlips  at 45°C for 24 h using 1 µg of each probe diluted in 50 μl of hybridization buffer  for each section. Subsequently, sections were washed six times with 1× PBS. Nonspecific autofluorescence of mite tissue was reduced by applying the Vector TrueView autofluorescence quencher kit from Vector laboratories  according to the manufacturer’s protocol. Finally, sections were mounted with the Vectashield Vibrance antifade mounting medium with 4′,6-diamidino-2-phenylindole (DAPI). Bright-field and fluorescence microscopy was performed using an Eclipse Ti fluorescence microscope  with a standard set of fluorescence filters.Bright-field microscopy of tissue sections showed that remains of the mites’ legs and dorsal shields still adhered to the semithin sections . As expeThe specificity of the used oligonucleotides was verified by FISH analysis of mites derived from a colony harboring a mite population that tested negative for DWV via RT-PCR (negative controls). FISH was performed without any oligonucleotide specific to DWV-A or DWV-B  or by appost hoc test using XLSTAT  software.Mite infestation rates, proportion of DWV-positive mites, proportion of DWV-infected mites, and proportion of crippled bees were analyzed with a one-way ANOVA and Fisher’s least significant difference (LSD) as


Vaccines are a recommended strategy for controlling influenza A infections in humans and animals. Here, we describe the effects of hydrostatic pressure on the structure, morphology and functional characteristics of avian influenza A H3N8 virus. The effect of hydrostatic pressure for 3 h on H3N8 virus revealed that the particles were resistant to this condition, and the virus displayed only a discrete conformational change. We found that pressure of 3 kbar applied for 6 h was able to inhibit haemagglutination and infectivity while virus replication was no longer observed, suggesting that full virus inactivation occurred at this point. However, the neuraminidase activity was not affected at this approach suggesting the maintenance of neutralizing antibody epitopes in this key antigen. Our data bring important information for the area of structural virology of enveloped particles and support the idea of applying pressure-induced inactivation as a tool for vaccine production. Alphainfluenzavirus genus into the Orthomyxoviridae family .The residual infectivity of the pressurized virus samples was assayed for three sequential blind passages. For each blind passage, the samples, which had no infectivity by TCID−1. This result indicates that few conformational changes have occurred to the exposed particles. Our data reveal a decrease of approximately 20 % in LS when pressure reached around 3 kbar.Previous studies have shown that hydrostatic pressure can be used to inactivate enveloped and non-enveloped RNA and DNA viruses . In this−1  dramatically decreased the virus litres in all cases.To investigate the effect of high pressure in the haemagglutinin activity we applied the haemagglutination test. Our data show that 3 h of applied pressure did not reduce the haemagglutinating activity of the virus particles. However, additional time of pressurization led to a complete loss of the haemagglutinating titre , suggestEntire virus particles that underwent pressurization were tested for a potential residual infectivity. For that, the pressurized preparation of virus particles was submitted to three serial passages in embryonated chicken eggs. Assay titration of pressurized viruses for 6 h showed an increase in titre after the first passage, which became higher at second and third passages . These rOur results show that the influenza virus has undergone conformational changes promoted by pressure as well as changes in function of their membrane glycoproteins. These observations are consistent with data showing that high hydrostatic pressure is able to promote modifications in the viral structure, which can lead to virus inactivation.Non-enveloped RNA viruses such human rhinovirus type 14 (HRV14) , foot-anThe effect of applying hydrostatic pressure for 3 h on H3N8 virus revealed that the particles were resistant to this condition, and the virus displayed only a discrete conformational change, as observed by bis-ANS fluorescence . Additio−1 [−1 [−1 [The pressure of 3 kbar alters the exposure of tryptophan residues of viral particles. Under the same conditions, the human rhinovirus 14 (HRV14) showed deviations of 350 cm−1 , the FMD−1 [−1 , and IBD [−1 [−1 . These d [−1 [−1 .This discrete structural change caused by hydrostatic pressure leads to virus inactivation. In the case of other pressure-inactivated viruses, such as vesicular stomatitis virus (VSV) or rotavirus, constant changes on the shape of viral particles and on the integrity of the membrane or the coat proteins were also observed . Envelopin vitro for its sialidase activity, which allows the removal of sialic acid residues from both haemagglutinin and neuraminidase spikes, as well as from cell surface glycoconjugates. Interesting, the pressure range used was not able to cause significative effect on the neuraminidase activity in all periods of time tested   and H3N8et al. , revealiet al. . Perhapset al. .The structures of the VSV were not dissociated after a long time of pressurization, but the subunits appear displaced from their normal positions, as shown by bulges under the envelope . PressurStudies with pressure-inactivated particles of yellow fever virus , infectiin vivo by blocking NA enzyme activity to prevent virion release and enhance Fc receptor-based activation of innate immune cells [The findings of this study showing that pressure does not act equally on HA and NA glycoproteins reveal that the technique presents some selectivity that might be a useful feature when considering it for developing a potential inactivated viral particle, as some desirable parts of the virus may still remain functional. For instance, whole enveloped particles of pressurized virus may preserve, probably by very subtle structural changes , the immne cells . Our dat