Approximately, 70% of cervical cancer cases worldwide are attributable to HPV-16 and HPV-18, with HPV-associated cancers being the second most common infection-related cancers globally. However, there´s paucity of data about this infective agent in Central Nigeria. In a cross-sectional study, we evaluated the seroprevalence of HPV-16 immunoglobulin G (IgG) and risk determinants among women in Central Nigeria as a first step towards evaluating anti-HPV IgM antibody for active cases and determining incidence. Blood samples were collected between August 2016 and January 2018, from 400 consenting women of childbearing age (15-49 years) who completed structured questionnaires. Samples were analyzed using HPV-16 specific IgG ELISA kits . Statistical analysis was performed to determine predictors. Overall, we found that 128 (32.0%) had IgG antibody against HPV-16. Seroprevalence by age was 50.0% (15-19 years), 55.0% (20-24 years), 12.9% (25-29 years), 50.0% (30-34 years), 32.1% (35-39 years), 18.2% (40-44 years) and 19.4% (45-49 years) respectively. Factors associated with infection were age , occupation , number of sex partners , history of genital warts  and education level . In addition, forty six (11.5%) reported having the history of genital warts with 268 (67.0%) and 132 (33.0%) subjects being married and single respectively. Individuals who were either artisans or civil servants were 260 (65.0%), whereas 140 (35.0%) were students. Majority, 324 (81.0%), had either primary, secondary or tertiary education with 76 (19.0%) of the subjects having no formal education. In respect of sexual behaviour, 196 (49.0%) reported having at least two sexual partners, out of which 64 (16.0%) had three or more. These findings provide high serological evidence of exposure to HPV-16 in Central Nigeria with implications for national and regional intervention initiatives. Limited data on human papillomavirus (HPV) is available in Nasarawa State and Central Nigeria in spite of the critical role this virus plays in cancer. Therefore, in the present pilot study which will lead to a more comprehensive investigation, including evaluating anti-HPV IgM antibody for active cases and determining incidence of infection, we found that the prevalence of IgG antibody to HPV-16 among women of child-bearing age who presented at a healthcare facility in Central Nigeria was 32.0%.HPV is a small non-enveloped icosahedral deoxyribonucleic acid (DNA) virus that can replicate in the nucleus of squamous epithelial cells, and infection with the virus is a major risk factor for squamous intraepithelial lesions and cervical cancer . The virGlobally, approximately 70% of all cases of cervical cancer are attributable to HPV-16 and HPV-18; and cervical cancer is the fourth most frequent cancer among women worldwide ,4. In NiMoreover, about 80% of HPV-attributable cancer cases occur in developing countries, with sub-Saharan Africa, Melanesia, Latin America and the Caribbean, south-central and south-east Asia having the highest incident cases . SeveralNotwithstanding the critical role of HPV in cancers, especially those of the cervix, there is a paucity of published data on HPV infection and risk determinants among women in Central Nigeria in spite of the public health significance of such evidence. Therefore, in the present pilot study, we evaluated exposure to HPV-16 by determining the prevalence of HPV-16 specific immunoglobulin G (IgG) antibody. We further assessed risk determinants among women of child-bearing age who presented at a healthcare facility in Central Nigeria. This allows for a more comprehensive study that will involve identifying the proportion of women with active cases (IgM antibody) and as well evaluating the incidence of infection to determine the level of risk posed to the population. As with other developing countries, such information is critical for intervention initiatives in Nigeria where knowledge of prevention initiatives and prophylactic vaccine availability have been found to be low among women .Study area: the healthcare facility where the study participants were recruited was located in Keffi Town, Nasarawa State. Keffi is approximately 68 km away from Abuja, the capital city of Nigeria. Keffi is located between latitude 8 5´N and longitude 7 8´E and situated on an altitude of 850 m above sea level [ea level .Ethical approval and informed consent: prior to the study, ethical clearance (ref: FMC/KF/HREC/098/16) was obtained from the Health Research Ethics Committee (Reg. No. NHREC/21/12/2012) at the Federal Medical Centre, Keffi, Nigeria, in line with the national code of ethics for biomedical research involving human subjects and the Helsinki Declaration. Informed consent was also obtained from each participant before enrollment. This was done by ensuring that each subject read and signed a consent form or had a translator read it for them before appending their signatures.Study population: we arrived at a representative sample size using the formula propounded by Naing as previously described [escribed . The stuExclusion and inclusion criteria: women who had history of HPV vaccination were excluded from the study. This ensured that only individuals who had anti-HPV-16 IgG antibody due to natural infection were included in the study.Sample collection: 5 ml of blood was collected aseptically from each participant by venipuncture into a sterile plain universal container. The blood was allowed to clot for 30 minutes and centrifuged at 3,000 rpm for 20 minutes. A Pasteur pipette was used to harvest and dispense each serum into a separate, properly labeled sample vial and stored at -20° C until use.Anti-HPV-16 IgG antibodies detection: the HPV-16 specific IgG ELISA Kits  were used to detect anti-HPV IgG antibody in the sera of subjects. The test procedure and result interpretation were carried out according to the manufacturer´s protocol. Included in the kits are negative and positive controls; and microtiter plates pre-coated with HPV-16 antigens. After the addition of uniformly diluted sera to the microtiter wells and 30-minute incubation at 37°C, wells were washed. This was followed by adding horseradish peroxidase (HRP)-conjugated anti-human IgG and a 30-minute incubation at 37°C. It was then washed thoroughly. The addition of tetramethylbenzidine (TMB) substrate solution to each well was done and termination of the enzyme-substrate reaction was effected by adding sulphuric acid solution. A microplate reader  was used at 450 nm to spectrometrically measure the intensity of colour changes. Manufacturer´s protocol was then used to determine, through optical density, the valence of anti-HPV-16 IgG antibody and the cut-off value for a positive HPV-16 result.Statistical analysis: descriptive statistical analysis was performed on data using the Smith´s Statistical Package Version 2.80  and Chi-squares (χ2) were calculated. The p-values and 95% confidence interval (CI) were determined for each of the variables . Associations between sero-positivity for HPV-16 IgG antibodies and the tested variables were evaluated using Chi-square tests. An association was considered statistically significant when p ≤ 0.05.A total of 400 women of child-bearing age with a mean age of 35.2 years voluntarily participated in this study. Overall, 128 (32.0%) had IgG antibody against HPV-16. Seroprevalence in relation to age was 50.0% (15-19 years), 55.0% (20-24 years), 12.9% (25-29 years), 50.0% (30-34 years), 32.1% (35-39 years), 18.2% (40-44 years) and 19.4% (45-49 years) respectively. In addition, forty-six (11.5%) reported having the history of genital warts with 268 (67.0%) and 132 (33.0%) subjects being married and single respectively. Individuals who were either artisans or civil servants were 260 (65.0%), whereas 140 (35.0%) were students. Majority, 324 (81.0%), had either primary, secondary or tertiary education with 76 (19.0%) of the subjects having no formal education. In respect of sexual behaviour, 196 (49.0%) reported having at least two sexual partners, out of which 64 (16.0%) had three or more .In this study, we found high serological evidence of exposure to HPV-16 to be 32.0% by determining the proportion of individuals who had HPV-16 specific IgG antibody among women of reproductive age who presented at a healthcare facility in Central Nigeria. However, this does not represent the total burden of infection since a study to identify active (IgM antibody) and incident cases is underway. Nevertheless, the evidence of exposure recorded in this study, defined as being HPV-16 IgG antibody positive, is high in comparison to similar studies carried out in certain parts of Southern Nigeria. For instance, it was 23.6% in Osogbo and 10% in Port Harcourt ,14. MoreThe distribution of HPV infection according to age appeared to be high in all age groups and there was a statistically significant association between age and infection (p < 0.05). The high prevalence in all age groups agrees with a previous study in Southern Nigeria , and undWith respect to occupation, anti-HPV-16 IgG antibody prevalence was 76.3%, 47.1% and 2.2% among civil servants, students and artisans respectively; with this variable being a factor associated with infection (p < 0.05). Moreover, our findings revealed a statistically significant higher prevalence among uneducated subjects and those with only primary education. The fact that these two groups of individuals lack basic education that guarantees access to prevention information resources may be a suitable explanation for this observation. There was a statistically significant association between the number of sexual partners and the risk of exposure (p < 0.05). This was no surprise in view of the relationship between HPV and sexual activities. Moreover, our findings show significant relationship (p < 0.05) between the history of genital warts among subjects with sero-positivity of HPV-16 IgG antibodies. This further confirms the association of HPV with genital warts which typically occurs on the vulva, cervix, vagina and around the anus of infected women.This study demonstrates high serological evidence of exposure to HPV-16 among women of reproductive age within the study area; and the circulation of this virus within the population portends grave public health consequences. Importantly, with growing scientific evidence linking HPV to cervical and anogenital cancers  as well as some head and neck cancers, this study undoubtedly provides critical information that will inform cancer prevention policy. Findings in this pilot study provide critical insights into the burden of HPV infection in a healthcare setting in Central Nigeria with implication for national and regional intervention initiatives, including prophylactic vaccination and other prevention services.HPV-16 and HPV-18 are associated with about 70% of cervical cancer cases globally, and the second most common infection-related cancers are HPV-associated;Among women worldwide, cervical cancer is the fourth most frequent cancer and much of the burden of cancer among women in Nigeria are attributable to HPV;HPV-16 is the most frequently isolated among cervical cancer patients out of the over 120 types of HPV that have been identified to date.This study demonstrates high serological evidence of exposure to HPV in the study population and provides the basis for evaluation of the incidence of infection;Insights into the burden of HPV infection in the study area is provided to inform local and regional intervention initiatives;It provides baseline data that can inform further studies.


It is co-authored with two Veterans who are involved in recruitment and retention of Veterans to the VEG.Of Veterans, 10.2% experience homelessness as adults with high rates of illness and substance use and with 35% reporting use of ED services in 2019.10 The mission of the COE’s Research Division includes a focus on stakeholder engagement, with dedicated funds for the VEG’s formation and operation.2The COE was established in 2018 to improve resilience and recovery of Veterans with behavioral health challenges  through research and provider training activities at VA of Greater Los Angeles (VAGLA).11 Most VEG participants used VA homeless services and have a history of behavioral health challenges; many suffer from serious physical ailments, such as chronic pain.VEG participants reflect the demographics of Veterans served at VAGLA. Of the 10 Veterans who have served on the VEG, 7 were men  between the ages of 30 and 68, with an average age of 45; 3 were women between the ages of 39 and 68, with an average age of 53. Four identified as Black, 4 as White, 1 as multi-racial, and 1 undisclosed. For comparison, in FY 2019, VAGLA provided services to 16,000 homeless-experienced Veterans, 9% were women with an average age of 47, and 91% were men with an average age of 57.Veterans are recruited to the VEG via word of mouth and recommendations from homeless program clinicians. Participation can be a one-time event  or longitudinal. VEG meetings were initially held 6–10 times a year, with 3–5 present at a VEG meeting, ≥2 COE investigators, and 2 COE staff. To encourage participation, COE staff provide frequent meeting reminders, often contacting Veterans 3–5 times to ensure their attendance and providing transportation via bus vouchers. Veterans receive a $50 gift card for their counsel, an amount higher than the $5–20 per hour typical for participation in research studies.10The COE’s leadership worked with Veterans to develop the VEG’s process: VEG facilitators gave Veterans an orientation and a meeting outline, and explicitly encouraged all viewpoints and questions. Veterans served as members of the pilot study review team and in a consulting role for researchers with COE funding. Investigators seeking COE funding for pilot research projects were required to present proposals to the VEG and incorporate Veterans’ feedback. At the conclusion of these studies, researchers provided findings to the VEG to assist with the dissemination of findings. This process created a feedback loop between Veterans and researchers: Veterans saw how their feedback shaped the research process and the study outcomes, and researchers utilized their feedback to adapt and align projects to fit the needs of the Veteran community.10 Thus, facilitators changed the process to more fully orient researchers to the VEG’s mission and goals and to encourage them to solicit specific feedback on aspects of the presented study. They also created a less structured format allowing Veterans to openly discuss their thoughts on each proposal. Some Veterans adopted informal facilitator roles to ask questions of researchers to translate aspects of their proposals to fellow Veterans, when they seemed unsure of what was being discussed. This modified approach enabled differing forms of expertise to be recognized.Investigators modified meeting proceedings based on participating Veterans’ recommendations. During the first year of operation, researchers struggled to translate study proposals to lay audiences, while Veterans were not familiar with the traditional academic model of assessing the merits of an approach during the review process.4 They reported a sense of camaraderie in sharing their challenges accessing VA services and validation in knowing that researchers wanted to incorporate their perspectives. For these reasons, some Veterans felt the meetings served as a therapeutic space for them to “bring their full selves to the table.” Despite these successes, over 2 years, 4 Veterans stopped attending due to loss of contact, moving residences, or incompatible work schedules.Since the VEG’s creation in 2018, Veterans have advised VA researchers and clinicians on a range of topics, from feedback on a pilot intervention for Veterans who hear voices to a family resilience program for homelessness-experienced families. In total, they have consulted on 6 proposed studies. Veterans noted helping fellow Veterans and improving systems of care as motivations for participation.7 Researchers working with structurally vulnerable Veterans must be attentive to ethical issues related to economic exploitation and systemic racism, alongside other forms of discrimination.12 They must also pay special attention to power dynamics associated with compensation, homelessness, and communication, including Veterans’ understanding of research issues and language.4Homeless-experienced Veterans with behavioral health needs experience more structural vulnerability and discrimination than middle-class Veterans who often comprise VEGs.14 and that the amount should be similar to other research centers at UCLA and VAGLA. Likewise, Veterans, particularly those living in VA transitional housing, report that compensation is fair and a lifeline for them, enabling them to purchase necessities. Some suggest that increasing the amount, especially for those with children, may incentivize long-term participation of a diverse group of Veterans. Veterans note the hospitality felt while sharing refreshments in meetings, as a welcoming gesture that adds to their comfort.COE investigators understand Veterans’ contributions as work and believe that compensation demonstrates respect for participants’ time,15 Additional training and funding for COE investigators to develop meaningful roles for Veteran partners throughout proposed studies could enable greater partnership.16Meeting adaptations made in the early years of the VEG suggest a need to improve researchers’ ability to communicate clearly with lay audiences and develop infrastructure to ensure Veterans’ comprehension of proposed studies when providing feedback. To improve shared understanding between researchers and laypeople, a recent article on community engagement recommends the following: 1) modification of research proposals to a third to eighth-grade reading level; 2) development of a community board to review academic literature rewritten for lay audiences and summarize key points to researchers, before use in community forums; and 3) use of a trained group facilitator who is a representative community member.7VEG facilitators note Veterans’ housing status as a major barrier to sustained partnerships. Because many Veterans are recruited from VA transitional housing programs and clinical services, this population is mobile and may move far away from the meeting site. Veterans suggest that having additional correspondence with staff between meetings and technical support to join virtual meetings could support continued participation. Transportation issues, challenges navigating the campus, lack of reliable phone/Internet service, and childcare needs present additional challenges to Veteran engagement and factored into membership decline, particularly during COVID-19.16 Plans to recruit and pair interested Veterans with related lived experience as consultants to COE-funded researchers were not fully actualized; investigator guidelines to request UCLA and VA Institutional Review Boards’ permission for Veterans to consult on data analysis or anonymized pre-publication manuscripts, as a part of their research protocols, have not yet been fully developed. Veterans also expressed the need to establish personal relationships with researchers and staff, to develop a stronger sense of trust and value when offering their unique perspectives at group proceedings. Additional training and funding for COE researchers to develop meaningful roles for Veteran partners throughout the course of proposed studies could also enable greater partnership and shared leadership in research processes.18While the COE has resources to enable Veterans to provide guidance on a project from start to finish, the COVID-19 pandemic resulted in delays to the implementation of COE-funded pilot projects, scheduled VEG meetings, and plans to actualize coequal partnership. This limited Veterans’ ability to participate as shared leaders in all stages of the process, including research design, data collection, and analysis, and community outreach to share study findings.19 further integration of Veterans into COE organizational structure and workforce could help prevent their “tokenization.”14 Veterans with severe psychiatric disabilities, severe substance use disorders, and homelessness histories ought to be actively recruited as research staff, early career scholars, and mid-level scholars at the COE to produce research that represents the lived experiences of stakeholders.19 While the COE has Veterans on staff, targeted recruitment of structurally vulnerable Veterans and the development of a flexible, accessible work environment have not yet been achieved.Because traditional advisory roles tend to be low-frequency consultation activities,11 In the COE’s VEG, structurally vulnerable Veterans demonstrate altruism and a willingness to support research processes. This paper suggests that Veterans’ engagement throughout research projects could enable more equitable partnerships and shared leadership between researchers and Veterans. Researchers may also benefit from additional training and support to translate research to lay audiences. Lastly, Veterans may begin to set research priorities via additional community engagement strategies such as patient involvement, co-production, and community bioethics dialogues and by the development of a staff and investigator workforce that mirrors the population served.20 These approaches may support Veteran leadership as integral to research design and implementation. As institutional support for collaborative methodologies increases, addressing the translational and structural barriers to full Veteran partnership is crucial to the production of equitable research.Although new research engagement panels with homeless-experienced Veterans are forming at the VA, little has been published about best practices when working with this population in VEGs.


Biochemical, molecular and genetic approaches show that each CRISP protein participates in more than one stage of gamete interaction  by either ligand-receptor interactions or the regulation of several capacitation-associated events  likely through their ability to regulate different sperm ion channels. Moreover, deletion of different numbers and combination of Crisp genes leading to the generation of single, double, triple and quadruple knockout mice showed that CRISP proteins are essential for male fertility and are involved not only in gamete interaction but also in previous and subsequent steps such as sperm transport within the female tract and early embryo development. Collectively, these observations reveal that CRISP have evolved to perform redundant as well as specialized functions and are organized in functional modules within the family that work through independent pathways and contribute distinctly to fertility success. Redundancy and compensation mechanisms within protein families are particularly important for spermatozoa which are transcriptionally and translationally inactive cells carrying numerous protein families, emphasizing the importance of generating multiple knockout models to unmask the true functional relevance of family proteins. Considering the high sequence and functional homology between rodent and human CRISP proteins, these observations will contribute to a better understanding and diagnosis of human infertility as well as the development of new contraceptive options.Mammalian fertilization is a complex process involving a series of successive sperm-egg interaction steps mediated by different molecules and mechanisms. Studies carried out during the past 30 years, using a group of proteins named CRISP (Cysteine-RIch Secretory Proteins), have significantly contributed to elucidating the molecular mechanisms underlying mammalian gamete interaction. The CRISP family is composed of four members  in mammals, mainly expressed in the male tract, present in spermatozoa and exhibiting Ca In mammals, sperm that leave the testes are not capable of recognizing and fertilizing the egg. In order to acquire fertilizing competence, sperm must undergo several physiological changes during their transit through the male and female reproductive tracts, known as sperm maturation  and sperFor more than 30 years, our laboratory has been dedicated to elucidate the molecular mechanisms involved in the mammalian fertilization process using as a model the evolutionarily conserved Cysteine-RIch Secretory Protein (CRISP) family, a group of highly homologous proteins enriched mainly in the mammalian reproductive tract and the venom of reptiles . The CRICRISP1, the first member of the family, was identified in the rat epididymis and originally named DE . It is a2+ channel located in both the sperm head and tail plasma membranes, and proposed to regulate the progesterone- and ZP-induced acrosome reaction  , is a no2+ RyR channels  which exhibit different phenotypes described in detail in the following section.Crisp1 locus but it is modulated by the genetic context. Of note, in spite of the Ca2+ channel regulatory activity described for CRISP1  does not support a critical role for CRISP3 in fertilization.In contrast to the rest of the CRISP family members, there is little information on the relevance of CRISP3 for fertilization and fertility. Although a recent work reports that provided . In thisCrisp4 single knockout males were also found to be fertile even when generated using different strategies and genetic backgrounds  , likely channels .Crisp family genes.However, in spite of the critical roles of CRISP proteins in different stages of fertilization, all single knockout animals were fertile, supporting the existence of functional overlapping or redundancy among CRISP family members. In this regard, the development of mutant mice has revolutionized the reproductive field showing that only a small number of the proteins previously known to play an essential role in the fertilization process were indeed essential for fertility in mice . A possiCrisp2 and Crisp4 are located in different chromosomes together with the availability of CRISP2 and CRISP4 single knockout colonies, led our laboratory to generate double Crisp2−/−/Crisp4−/− mice by natural mating . Although the reasons for the normal fertility of these mutant animals is still unknown, it is possible that the lack of epididymal CRISP4 is partially compensated by the presence of CRISP1, the other epididymal CRISP family member.The fact that l mating . Analysil mating . Neverthnt males . ConsistCrisp1−/−/Crisp4−/− colony exhibited a clear disruption of fertility .Both CRISP1 and CRISP4 are expressed in the epididymis in high concentrations , bind toertility . DiffereCrisp1−/−/Crisp4−/− males showed they exhibited an immature epididymal epithelium and abnormal luminal acidification, contributing to a better understanding of the fine-tuning mechanisms underlying epididymal sperm maturation  males deficient in the four CRISP members showed a dramatic inhibition in their fertility with an average of less than one born pup and a high proportion of sterile males  (in vivo fertilization failure is mainly due to sperm defects in those events that precede gamete fusion such as sperm migration within the oviduct and penetration of the egg coats.In addition to these KO sperm . The finsp4−/−) . Althougsp4−/−)  and CRISsp4−/−)  and/or tsp4−/−)  known tosp4−/−) . Interes2+ channels and the relevance of this cation for most sperm functional events, QKO sperm did not show the characteristic intracellular Ca2+ increase that occurs during sperm capacitation, indicating that multiple mutant sperm exhibit a dysregulation of Ca2+ homeostasis that probably reflects the final balance of the individual contribution of each CRISP to Ca2+regulation. Finally, multiple mutant males exhibited clear embryo development defects as those previously described for the Crisp1−/−/Crisp3−/−colony  through different mechanisms that include ligand-receptor interactions as well as regulation of several capacitation-associated events , likely through their ability to regulate different CaEvidence supports the idea that CRISP proteins have evolved to perform redundant as well as specialized functions to ensure fertility success and are organized in functional modules within the family that work through independent pathways and contribute distinctly to fertility success . In thisRedundancy and compensatory mechanisms like those observed within the CRISP protein family are particularly important in the case of spermatozoa which are transcriptionally and translationally inactive cells and carry several protein families  to guarantee their functionality. This emphasizes the importance of generating multiple knockout of family genes since single knockout models might be masking the true functional relevance of family proteins.Considering the high sequence and functional homology between rodent and human CRISP proteins, it is likely that the same redundant and specific mechanisms operate within the human CRISP family giving rise to the same functional modules . Furthermore, as the three hCRISP genes are located very close to each other within the same chromosome, it is possible that a single rearrangement in that region is responsible for some cases of unexplained infertility due to the simultaneous absence of more than one human CRISP protein, supporting the relevance of our observations for the diagnosis and treatment of human infertility as well as for the development of new non-hormonal contraceptive options.


Women with HIV/HPV coinfection and cervical lesions are at increased risk of developing HPV related anal cancer. Self-collection of anal swabs may facilitate HPV molecular testing in anal cancer screening, especially in high-risk groups, and yet it is not adequately studied. We evaluated level of agreement between self-collected anal swabs (SCAS) and clinician-collected anal swabs (CCAS) when used for HPV genotyping. We also described the anal HPV genotype distribution and HIV/HPV coinfection.We performed a cross sectional study with participants from a visual-inspection-with-acetic-acid and cervicography (VIAC) clinic, in Harare, Zimbabwe. In a clinic setting, the women aged ≥18 years provided anal swabs in duplicate; first CCAS and then SCAS immediately after. HPV detection and genotyping were performed using next generation amplicon sequencing of a 450bp region of the HPV L1 gene. Level of agreement of HPV genotypes between CCAS and SCAS was calculated using the kappa statistic. McNemar tests were used to evaluate agreement in the proportion of genotypes detected by either method.Three-hundred women provided 600 samples for HPV genotyping. HPV genotypes were detected in 25% of SCAS and in 22% of CCAS. The most common genotypes with CCAS were HPV52, HPV62 and HPV70 and with SCAS were HPV62, HPV44, HPV52, HPV53 and HPV68. Total HPV genotypes detected in CCAS were more than those detected in SCAS, 32 versus 27. The agreement of HPV genotypes between the two methods was 0.55 in kappa value (k). The test of proportions using McNemar gave a Chi-square value of 0.75 (p = 0.39). Multiple HPV infections were detected in 28/75 and 29/67 women for CCAS and SCAS respectively.SCAS and CCAS anal swabs showed moderate agreement, with no statistically significant difference in the proportion of genotypes detected by either methods. Although the differences between the two methods were not statistically significant, CCAS detected more HPV genotypes than SCAS and more HPV infections were detected in SCAS than in CCAS. Our data suggest that self-collected anal swabs can be used as an alternative to clinician-collected anal swabs for HPV genotyping. Given increasing incidence of anal cancer worldwide and new guidelines for anal HPV screening, self-sampling may help screening programs achieve greater coverage. Thus, there is a need for research regarding utility of self-sampling vis a vis clinician sampling. I have the following comments and suggestions:AbstractI suggest changing the last sentence to, “Our data suggest that self-collected anal swabs can be used as an alternative to clinician-collected anal swabs for HPV DNA testing in a clinical setting.”IntroParagraph 1 would benefit from mention of burden of disease. I suggest including data on burden of cervical cancer, narrowing in on burden is sub-Saharan Africa.Paragraph 2 “Although anal cancers are relatively rare, data from USA reports a gradual increase in the incidence of anal cancers especially in HIV-infected individuals, regardless of the antiretroviral (ART) era [5]. Furthermore, a cumulative incidence of 0.1% by age 75 years wasreported in HIV uninfected individuals as compared to 1.5% in HIV infected individuals.https://doi.org/10.1093/jnci/djz219]. The increase is particularly high among HIV-infected individuals in the anti-retroviral era[include data on increasing incidence].The increase in anal cancer seems to be broader than among HIV-infected individuals. I suggest revising to: Although anal cancers are relatively rare, data from USA indicates a significant increase in the incidence of anal cancers .” I’m not sure that it’s “regardless” of the anti-retroviral era, rather than “in” the antiretroviral era. Isn’t the extension of life due to ART driving increasing cancer incidence among HIV+ individuals?Paragraph 1 and 2 jump around quite a bit. Also, since the paper doesn’t seek to fill the gap in data regarding burden of anal cancer in Zimbabwe, I don’t think it makes sense to set this up as an argument in the Intro. How about ending paragraph 1 with “Women with a history of cervical cancer, especially those with HPV/HIV co-infection, are at increased risk of developing anal cancers [4]. Screening for anal cancer is thus recommended for women with cervical lesions and/or who are HIV infected .” And starting paragraph 2 with “Although anal cancers are relatively rare, data from USA indicates a significant increase in the incidence of anal cancers. The increase is particularly high among HIV-infected individuals in the anti-retroviral era. Zimbabwe has an HIV prevalence of almost 13% and cervical cancer contributes a third of all cancers among black Zimbabwean women. In 2016, the Zimbabwe Cancer Registry reported a gradual increase in anal cancers recorded in the past decade. Despite the increased prevalence of risk factors in the population and evidence of increasing incidence, anal cancer screening guidelines are not routinely followed in Zimbabwe.”Given focus of paper on HPV genotypes and multiple infections, it would be helpful to reader to understand why different genotypes matter. Could this be woven into the intro? This is mentioned in Discussion, but I’d move to IntroParagraph 3 jumps between accuracy and acceptability and between anal and cervical swabs. I suggest walking the reader through the arguments to better set up the rationale for the study. Eg. “Utility of self-sample cervical swabs for HPV DNA testing has been demonstrated. Furthermore, self-collection of cervical swabs has shown to be highly acceptable. For anal screening, there is evidence that self-sampling is acceptable and patients tend to be more comfortable and less embarrassed when an anal swab is self-collected. Its clinical utility has been demonstrated for non-HPV studies [sidenote: which tests?] and for cytology. However, here is still scarce data with regards to self-collected sample for HPV DNA testing.”MethodsLaboratory Methods—DNA extraction. Is this per manufacturers’ instruction? If so, I ‘m not sure that this level of detail is needed.ResultsThe results and (discussion) seem to jump back and forth between describing HPV genotypes and presence of HPV DNA. As written, I can’t follow where kappa statistic is for presence of HPV DNA or for specific genotypes.DiscussionPostulate 3 seems very unlikely.Paragraphs 7 and 8 (lines 338-353) seem to go beyond the data and focus of the paper. Given this, and that Discussion gets quite lengthy, I’d suggest omitting these paragraphs.Conclusion: “Cautiously recommend…” should be replaced with “Our data suggest that…” (see comments on abstract).Reviewer #2: The authors of this generally well-written manuscript were interested in assessing potential anal cancer screening methods that focus on exfoliated cell collection from the anal canal. They compared clinician-collected vs self-collected anal swabs (CCAS vs SCAS) from women attending a cervical cancer screening program in Zimbabwe. The analysis found higher HPV prevalence in SCAS but a higher number of genotypes in CCAS. The method for HPV detection was next generation sequencing and this method leads to a number of questions about the results. At times, the attention to differing options for cut-off read numbers (100 vs 500 vs 1000) obscures the HPV results and calls into question the method of detecting HPV. And if the paper doesn’t have a sound method for detecting HPV, then the HPV results that depend on that detection method, e.g., comparisons of CCAS and SCAS, are called into question. Overall recommendation is to decide which cut-off level is best, defend that decision in the methods with literature, and then report results only for that cut-off level. Until that cut-off level is understood to be clearly the right one, then recommendations for anal cancer screening based on these data may be inappropriate. In addition, since anal cancer screening methods is the reason this study was done, the analysis needs to pay more attention to reporting results of high-risk HPV and results within HIV-positive people.Abstract:L53 – focus these results on high-risk types and difference by HIV status.Methods:L134 – why were Dacron swabs chosen over other options like flocked swab?L135 – who did the breaking of the swab into the cryovial? Participant or staff?L177 – why is 500 better than 100 or 1000? It seems to me that the results can have very different interpretations if, say 100, is chosen instead of 500. There is speculation about false-positive and false-negative results in the discussion, but it seems this should be clearly laid out by the authors in the methods.L180 – it would be nice to see simple agreement in addition to kappa (agreement beyond chance).L181 – 183 – this sentence is difficult to understand.L_ - most assays assess whether or not a sample is adequate for testing. How is this assessed with NGS? Is it possible that a participant could have waived the swab in the air and this swab was judged to be HPV-negative by the authors?Results:Table 1 – what kind of contraception for the Yes group? Does the multiple sexual partners variable mean the participant acknowledged having >1 concurrent partner at recruitment?Supp table 2 I don’t understand the heading: “Number of positive CCAS and SCAS GENOTYPES with cut-off……” Do you mean, “Number of HPV positive CCAS and SCAS specimens with cut-off……”?Figure 1 A CCAS - HPV16 is typically the most prevalent genotype in other studies as it almost is for CCAS at the 100 cut-off. And it certainly is the most important type for anal cancer. Why not give preference to the most sensitive scenario for detecting HPV16? i.e., choose 100 as the cut-off. The authors state there may be too many false-positives; but the paper doesn’t seem to have a convincing argument that these HPV16 reads are mostly false-positive. Also, since you’re reporting data for three cut-offs, and this is not a methods paper about cut-offs, the message of this figure is that reasonable persons might believe that any one of these 3 cut-offs is closer to the truth.Fig 2 A and B – the grid lines fall in odd intervals making it tough to assess the frequency for any given column. B – This figure makes no sense to me. It does not communicate the level of concordance in any way that I can understand.L207 – “type distributions were similar regardless of …cutoffs”….this doesn’t seem to be true since HPV16 – the most important type for anal cancer - has a prevalence of ~13% in CCAS with 100 reads. Prevalence of HPV 16 is otherwise 5 or 6 percent.L209 – reason for choosing 500 over 100 cutoff is very briefly addressed but reason for choosing 500 over 1000 is not addressed. Again, it seems this should be addressed in the methods.L221 – overall positivity for each swabbing group is central to this paper and should appear in a table or figure. There are too many data in the results narrative that are not included in a table or figure. In this area I would also expect to see results that are specific to high-risk types since it’s a cancer outcome that the authors care about most.L227 – why calculate kappa for all genotypes when only a few are responsible for almost all anal cancer?L252 – It would be nice to see these data in a table stratified by HIV status.Discussion:L275 – Other studies have also compared CCAS and SCAS for cytology – Chin-Hong, 2008 and Cranston, 2004L302 – Add citation for claim that HPV53 is possibly carcinogenic.L312-313. If the observations are dependent as you suggest (which makes sense), then the kappa statistic is not appropriate since it requires independent observations. Add this to limitations.L328 – do you mean 40% of women with HPV had multiple infections?L360 – this range is troubling, because it implies that the McNemar test was almost significant at one of the cut-off thresholds (I presume 100), i.e., at one of the cut-off levels, the p-value was 0.06 for a difference between CCAS and SCAS.L361 – the authors indicate here that they have adjusted the methods of the study  in order to maintain statistical significance in their analysis. This is not appropriate. It brings me back to my central concern: that the authors need to justify which cut-off is most appropriate with literature. And if that’s not possible, then maybe a methods paper  is most appropriate for these data.L366. Other than limitation of funds, there is not a clear listing of limitations of this study. One of these might be that kappa assumes the two raters are equally competent which is not the case here.https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool,  17 Nov 2020Dear Dr Michael ScheurerWe would like to thank you and the reviewers for the thorough assessment of our work and for the constructive feedback. In the following, we respond to all concerns and comments point-by-point. Editor commentsJournal RequirementsWhen submitting your revision, we need you to address these additional requirements.Editor point 1: Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found athttps://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf andhttps://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdfReply: We have now formatted and renamed our documents to ensure that they meet the journal’s style. Editor point 2: Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information.Reply: The questionnaire used in our study, written in both English and Shona, is now included as supplementary document 1. We have also indicated the inclusion of the document under section 2.1 L127-128. Editor point 3: In your Methods section, please provide additional information about the participant recruitment method and the demographic details of your participants. Please ensure you have provided sufficient details to replicate the analyses such as: a) a description of any inclusion/exclusion criteria that were applied to participant recruitment. b) a statement as to whether your sample can be considered representative of a larger population, c) a description of how participants were recruited, and d) descriptions of where participants were recruited and where the research took place.Reply: a-d) A line that briefly states that sexually active women aged at least 18 years old were reporting for routine cervical cancer screening were included is now captured in section 2.2 L145-150, whilst L124-129 inform the reader of how and where the study was carried out and to what extent the sample set was representative of a bigger population.Editor point 4: Please provide a sample size and power calculation in the Methods, or discuss the reasons for not performing one before study initiation. Reply: The sample size calculation is now detailed in section 2.1 L130-138. The formular accounted for a power of 0.80.https://journals.plos.org/plosone/s/submission-guidelines.#loc-statistical-reporting. Editor point 5: To comply with PLOS ONE submission guidelines, in your Methods section, please provide additional information regarding your statistical analyses, including the threshold set for statistical significance for the analyses. For more information on PLOS ONE's expectations for statistical reporting, please see Reply: The authors have a working R-script that can be made available upon the readers’ requests directly from the corresponding author. However a summary of the analyses performed on R-Studio is now included on section 2.2.2 L192-213.Editor point 6: In the Methods section, please provide the specific sequences of the primers used in the next-generation sequencing analysis.Reply: We have now included specific sequences of the primers as Table 1. L188[Note: HTML markup is below. Please do not edit.]Reviewer #1 commentsReviewer #1: This is an interesting manuscript describing concordance between self- and clinician-collected anal swabs for HPV DNA testing. Given increasing incidence of anal cancer worldwide and new guidelines for anal HPV screening, self-sampling may help screening programs achieve greater coverage. Thus, there is a need for research regarding utility of self-sampling vis a vis clinician sampling. I have the following comments and suggestions:AbstractReviewer #1: I suggest changing the last sentence to, “Our data suggest that self-collected anal swabs can be used as an alternative to clinician-collected anal swabs for HPV DNA testing in a clinical setting.”Reply: We have now incorporated the suggested wording on L61-63 IntroductionReviewer #1: Paragraph 1 would benefit from mention of burden of disease. I suggest including data on burden of cervical cancer, narrowing in on burden is sub-Saharan Africa.Reply: We have now included facts on the burden of disease in Low-middle income countries and in Zimbabwe. This is captured on L75-78.Reviewer #1: Paragraph 2 “Although anal cancers are relatively rare, data from USA reports a gradual increase in the incidence of anal cancers especially in HIV-infected individuals, regardless of the antiretroviral (ART) era [5]. Furthermore, a cumulative incidence of 0.1% by age 75 years was reported in HIV uninfected individuals as compared to 1.5% in HIV infected individuals.https://doi.org/10.1093/jnci/djz219]. The increase is particularly high among HIV-infected individuals in the anti-retroviral era[include data on increasing incidence].The increase in anal cancer seems to be broader than among HIV-infected individuals. I suggest revising to: Although anal cancers are relatively rare, data from USA indicates a significant increase in the incidence of anal cancers .” I’m not sure that it’s “regardless” of the anti-retroviral era, rather than “in” the antiretroviral era. Isn’t the extension of life due to ART driving increasing cancer incidence among HIV+ individuals?Reply: We are grateful for the suggestions and we have now incorporated them on L84-86. We have also cited the paper by Deshmukh et al. Regarding the side note, we used ‘regardless of the ART era’ to indicate that in as much as ART is meant to improve the immunological profiles of an individual, we still have consistent HPV infections leading to cancer. The reviewer points out a different school of thought that describes the extension of life, due to ART, leading to cancer development. Both points are now integrated and captured in L85-88.Reviewer #1: Paragraph 1 and 2 jump around quite a bit. Also, since the paper doesn’t seek to fill the gap in data regarding burden of anal cancer in Zimbabwe, I don’t think it makes sense to set this up as an argument in the Intro. How about ending paragraph 1 with “Women with a history of cervical cancer, especially those with HPV/HIV co-infection, are at increased risk of developing anal cancers [4]. Screening for anal cancer is thus recommended for women with cervical lesions and/or who are HIV infected .” And starting paragraph 2 with “Although anal cancers are relatively rare, data from USA indicates a significant increase in the incidence of anal cancers. The increase is particularly high among HIV-infected individuals in the anti-retroviral era. Zimbabwe has an HIV prevalence of almost 13% and cervical cancer contributes a third of all cancers among black Zimbabwean women. In 2016, the Zimbabwe Cancer Registry reported a gradual increase in anal cancers recorded in the past decade. Despite the increased prevalence of risk factors in the population and evidence of increasing incidence, anal cancer screening guidelines are not routinely followed in Zimbabwe.”Reply: Paragraph 1 now ends with the sentence on screening for anal cancer and paragraph 2 begins with the incidence of anal cancer in USA. L82-86.Reviewer #1: Given focus of paper on HPV genotypes and multiple infections, it would be helpful to reader to understand why different genotypes matter. Could this be woven into the intro? This is mentioned in Discussion, but I’d move to IntroReply: We agree with the reviewer, for the reader to grasp the importance of reporting HPV genotypes right from the beginning, we have now moved the lines from discussion to the last paragraph of the introduction. L112-119.Reviewer #1: Paragraph 3 jumps between accuracy and acceptability and between anal and cervical swabs. I suggest walking the reader through the arguments to better set up the rationale for the study. Eg. “Utility of self-sample cervical swabs for HPV DNA testing has been demonstrated. Furthermore, self-collection of cervical swabs has shown to be highly acceptable. For anal screening, there is evidence that self-sampling is acceptable and patients tend to be more comfortable and less embarrassed when an anal swab is self-collected. Its clinical utility has been demonstrated for non-HPV studies [sidenote: which tests?] and for cytology. However, here is still scarce data with regards to self-collected sample for HPV DNA testing.”Reply: With the reviewer 1’s suggested phrasing, we have now re-written paragraph 3 and improved on the general flow. L95-100. MethodsReviewer #1: Laboratory Methods—DNA extraction. Is this per manufacturers’ instruction? If so, I ‘m not sure that this level of detail is needed.Reply: Yes, the extraction was as per manufacturer’s instruction. The extra detail on DNA extraction has now been deleted L164-166ResultsReviewer #1: The results and (discussion) seem to jump back and forth between describing HPV genotypes and presence of HPV DNA. As written, I can’t follow where kappa statistic is for presence of HPV DNA or for specific genotypes.Reply: To avoid losing the reader and to improve on the flow we have now used consistent terminology, “HPV genotypes” in all sections. The Kappa test is for presence of any HPV genotype.DiscussionReviewer #1: Postulate 3 seems very unlikely. Reply: We have kept postulate 3 in the text and added the word “unlikely” to guide the readers. L332Reviewer #1: Paragraphs 7 and 8 (lines 338-353) seem to go beyond the data and focus of the paper. Given this, and that Discussion gets quite lengthy, I’d suggest omitting these paragraphs. Reply: Paragraphs 7 describes the distribution of HPV genotypes by HIV status and paragraph 8 briefly describes cervical disease . Inasmuch as these two paragraphs mainly discuss secondary data, they are important for the reader to have a full perspective of the sample population. Given that women who have a history of cervical lesions and/or HIV co-infection are at increased risk of anal HPV infection. We have re-written the beginning of paragraph 8, L342, to capture the relevance of the paragraphs. Reviewer #1: Conclusion: “Cautiously recommend…” should be replaced with “Our data suggest that…” (see comments on abstract). Reply: We agree with the reviewer, therefore the conclusion is now phrased as ‘our data suggest that….’ L61 and L375.Reviewer #2 commentsReviewer #2: The authors of this generally well-written manuscript were interested in assessing potential anal cancer screening methods that focus on exfoliated cell collection from the anal canal. They compared clinician-collected vs self-collected anal swabs (CCAS vs SCAS) from women attending a cervical cancer screening program in Zimbabwe. The analysis found higher HPV prevalence in SCAS but a higher number of genotypes in CCAS. The method for HPV detection was next generation sequencing and this method leads to a number of questions about the results. At times, the attention to differing options for cut-off read numbers (100 vs 500 vs 1000) obscures the HPV results and calls into question the method of detecting HPV. And if the paper doesn’t have a sound method for detecting HPV, then the HPV results that depend on that detection method, e.g., comparisons of CCAS and SCAS, are called into question. Overall recommendation is to decide which cut-off level is best, defend that decision in the methods with literature, and then report results only for that cut-off level. Until that cut-off level is understood to be clearly the right one, then recommendations for anal cancer screening based on these data may be inappropriate. In addition, since anal cancer screening methods is the reason this study was done, the analysis needs to pay more attention to reporting results of high-risk HPV and results within HIV-positive people.AbstractReviewer #2: L53 – focus these results on high-risk types and difference by HIV status. Reply: We summarise the detection of high-risk HPV genotypes in the discussion section, L302-311 and L348-351. The primary aim and scope of this manuscript was to determine whether the same HPV genotypes were detected in self-collected and clinician-collected swabs, therefore we reported all the genotypes, regardless of whether they are high risk or low-risk. In addition, the most detected genotypes did not include a large number of high-risk genotypes. This is probably because these were mostly ‘disease free’ women reporting for routine screening, a good sample population for the purposes of primarily comparing CCAS to SCAS. We agree that in future studies, where we will focus on HPV genotype distribution other than comparison of collection methods, we can explore in-depth the anal high-risk HPV genotypes and HIV status.MethodsReviewer #2: L134 – why were Dacron swabs chosen over other options like flocked swab?https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717820/ and https://pubmed.ncbi.nlm.nih.gov/21791907/. In our setting dacron swabs are the most readily available synthetic swabs, therefore given their proven use, we chose them to avoid inconsistency. The likelihood of running out of flocked swabs and having to wait for very long periods for new procurements would have been high. The citations used for justifying the choice of dacron swabs are now included on L145.Reply: Our choice was based on literature that reported dacron and flocked swabs having harvested similar amounts of cells. Although in some scenarios flocked swabs are deemed superior, the difference with dacron swabs is minimal. Reviewer #2: L150 – who did the breaking of the swab into the cryovial? Participant or staff?Reply: The collection procedure was explained to all participants by the recruiting nurse. Self-collected swabs were broken into the tube by the participant, immediately after swabbing. Clinician-collected swabs were broken into the tube by the clinician as soon as they completed the swabbing. This is now indicated under section 2.2 L155.Reviewer #2: L177 – why is 500 better than 100 or 1000? It seems to me that the results can have very different interpretations if, say 100, is chosen instead of 500. There is speculation about false-positive and false-negative results in the discussion, but it seems this should be clearly laid out by the authors in the methods. https://pubmed.ncbi.nlm.nih.gov/31552176/. Although, there are a few papers that suggest varied cut-offs, Meisal et al DOI:10.1371/journal.pone.0169074 and Cullen et al doi: 10.1016/j.pvr.2015.05.004 , there is generally no consensus on the minimum required read counts using deep targeted sequencing therefore each laboratory sets its own parameters based on the depth of coverage, the average read pairs and the statistical analyses methods employed. We have now clearly presented our justification (L199-202) and consistently only reported results using a cut-off that’s at least 500 read pairs. Fortunately, one of the co-authors is now preparing a methods paper to suggest the best cut-offs for our laboratory.Reply: We agree with the reviewer that presenting more than 1 cut-off can be confusing to the readers, thus we have carefully chosen to report all our findings based on a 500 read pairs cut-off. Our choice is based on the analyses of our read pairs which had a mean of 26232 for CCAS and 19110 for SCAS. Due to the difference in means, instead of normalising we calculated for a slightly higher cut-off. Assuming limit of detection of 5%, our 500 cut-off allows us to filter any false positive results and aligns with clinical recommendations of 300-500 published by Petrackova and colleagues Reviewer #2: L180 – it would be nice to see simple agreement in addition to kappa (agreement beyond chance).https://pubmed.ncbi.nlm.nih.gov/18188809/ and https://pubmed.ncbi.nlm.nih.gov/10520333/. Reply: We present both the Cohen’s Kappa and the McNemer because they complement each other. Kappa assumes the two raters are equally competent whilst McNemar allows for unequal raters. We agree that the Kappa assumes the observed agreement to be due to chance. Therefore we included a McNemar test to enhance the agreement analysis and to ensure a more valid interpretation, L210. The McNemar assumes that HPV genotypes detected from self-collected swabs are equal to those detected by clinician-collected swabs. To the best of our knowledge, the complementary effect of these two tests is sufficient to describe the agreement of the collection methods Reviewer #2: L181 – 183 – this sentence is difficult to understand. Reply: The sentence has now been rephrased. We have now specifically described how the plots were made using the HPV genotype frequencies. L201-203.Reviewer #2: L_ - most assays assess whether or not a sample is adequate for testing. How is this assessed with NGS? Reply: NGS detects betaglobin as part of a control step to check if the DNA is adequate for testing. However, our samples were treated differently because they had already undergone betaglobin testing as an upstream procedure for a different assay (dot-blot-hybridisation) in Zimbabwe, for a different research scope. This was not repeated before NGS. We have now indicated this in the methods section. L166-168 Reviewer #2: Is it possible that a participant could have waived the swab in the air and this swab was judged to be HPV-negative by the authors? Reply: This is highly unlikely, because the participants had the procedure explained to them by the nurse, who also closely monitored any women who requested supervision. As soon as the swab was collected it was transferred into the cryotube.ResultsReviewer #2: Table 1 – what kind of contraception for the Yes group? Reply: This question referred to any type of contraception. A follow-up question also captured the specific contraception; however, this detailed information is not relevant for the scope of this manuscript. Please see question 14 of the questionnaire, attached as supplementary document 1.Reviewer #2: Does the multiple sexual partners variable mean the participant acknowledged having >1 concurrent partner at recruitment? Reply: Yes, this is correct. The participants self-reported having more than 1 sexual partners at the time of recruitment. Please see the questionnaire attached as supplementary material on question numbers 9 to 11.Reviewer #2: Supp table 2 I don’t understand the heading: “Number of positive CCAS and SCAS GENOTYPES with cut-off……” Do you mean, “Number of HPV positive CCAS and SCAS specimens with cut-off……”? Reply: Thank you for this note, this was a typographic error. The caption for supplementary table 2 (which is now table 3) has now been corrected to “specimens” instead of “genotypes”. L226Reviewer #2: Figure 1 A CCAS - HPV16 is typically the most prevalent genotype in other studies as it almost is for CCAS at the 100 cut-off. And it certainly is the most important type for anal cancer. Why not give preference to the most sensitive scenario for detecting HPV16? i.e., choose 100 as the cut-off. The authors state there may be too many false-positives; but the paper doesn’t seem to have a convincing argument that these HPV16 reads are mostly false-positive. Also, since you’re reporting data for three cut-offs, and this is not a methods paper about cut-offs, the message of this figure is that reasonable persons might believe that any one of these 3 cut-offs is closer to the truth.Reply: We have considered your suggestions and settled for a cut-off of 500. This is based on the explanation given above, for your question on L177. Concerning HPV 16 prevalence, indeed there seems to be a reduction in the cases but it was not statistically significant. Furthermore, with NGS we expect the sensitivity to be standard for all genotypes. We are also of the view that presenting an optimum cut-off will be better regardless of the loss of seemingly ‘positive’ samples because if they do not meet the optimum cut-off, we consider them to be negative. We also agree that presenting more than one cut-off is not suited for the scope of this paper. These will now be presented in a different methods manuscript that some of the co-authors are working on. To avoid misleading the readers, we have removed Figure 1. This will be best suited for a methods manuscript.Reviewer #2: Fig 2 A and B – the grid lines fall in odd intervals making it tough to assess the frequency for any given column. B – This figure makes no sense to me. It does not communicate the level of concordance in any way that I can understand.Reply: The authors have taken a closer look at figure 2  and we agree that the way the frequencies were presented may have been confusing. We have now relabelled the y-axis to present frequencies as whole numbers as opposed to the 0.5 intervals. The main message conveyed by the figure is the difference of frequencies of the HPV genotypes detected by each method (A), whilst (B) further gives a pictorial illustration of instances when an HPV genotype was detected by either of the collection methods or by both. Reviewer #2: L207 – “type distributions were similar regardless of …cutoffs”….this doesn’t seem to be true since HPV16 – the most important type for anal cancer - has a prevalence of ~13% in CCAS with 100 reads. Prevalence of HPV 16 is otherwise 5 or 6 percent. L209 – reason for choosing 500 over 100 cutoff is very briefly addressed but reason for choosing 500 over 1000 is not addressed. Again, it seems this should be addressed in the methods.Reply: Similar to the response to Figure 1 above. We have now justified the use of 500 as a cut-off, therefore we have now discarded the need to compare HPV genotypes based on cut-offs, as we agree that this is not a methods paper.Reviewer #2: L221 – overall positivity for each swabbing group is central to this paper and should appear in a table or figure. There are too many data in the results narrative that are not included in a table or figure. In this area I would also expect to see results that are specific to high-risk types since it’s a cancer outcome that the authors care about most. Reply: Regarding the overall positivity for each swabbing group, we have now presented these in table 3 L229, previously labelled as supplementary table 1 and 2. We agree with the reviewer, cancer outcome is a critical end point which we wish to prevent by providing data that can offer more screening options. In the context of cancer development, high-risk genotypes have the most clinical relevance. However, the primary aim and scope of this manuscript was to determine whether the same HPV genotypes were detected in self-collected and clinician-collected swabs, therefore we reported all the genotypes including those with less clinical relevance. Having determined and described the agreement using a broad array of HPV genotypes, we envision that when applications are being made in a clinical setting, the clinician will receive a report specifying the clinically relevant HPV genotypes. Reviewer #2: L227 – why calculate kappa for all genotypes when only a few are responsible for almost all anal cancer?Reply: The reviewer has rightfully highlighted that high-risk HPV genotypes have the most clinical relevance. We used Illumina next-generation-sequencing which detects a broad array of HPV genotypes, thus our overall HPV anal tests should report good accuracy for all HPV genotypes. The primary aim and scope of this manuscript was to determine whether the same HPV genotypes were detected in self-collected and clinician-collected swabs, therefore we reported all the genotypes including those with less clinical relevance. Reviewer #2: L252 – It would be nice to see these data in a table stratified by HIV status.Reply: The scope of this manuscript is to compare two methods and we do not expect the HIV status of the women to affect the accuracy of the test, therefore we do not present the HPV genotype agreement of CCAS and SCAS by HIV status. However, we give a summary description of the HIV status of the sample population based on the gold-standard, which is the clinician-collected in this case. This gives the reader a good indication of the HPV/HIV co-infection in this group of women. Sections 3.3 L260-270.DiscussionReviewer #2: L275 – Other studies have also compared CCAS and SCAS for cytology – Chin-Hong, 2008 and Cranston, 2004Reply: Thank you for highlighting these important studies to us. The line has now been rephrased and the citations are now updated L98 and L282-283.Reviewer #2: L302 – Add citation for claim that HPV53 is possibly carcinogenic.Reply: A citation  has now been added and the phrase is also slightly modified to “probable high-risk”. L309-310.Reviewer #2: L312-313. If the observations are dependent as you suggest (which makes sense), then the kappa statistic is not appropriate since it requires independent observations. Add this to limitations. Reply: We have now highlighted this limitation on L363-370.Reviewer #2: L328 – do you mean 40% of women with HPV had multiple infections?Reply: Yes, 40% of women with HPV had multiple infections. We have added the phrase “of HPV infected” to clearly capture this L335.Reviewer #2: L360 – this range is troubling, because it implies that the McNemar test was almost significant at one of the cut-off thresholds (I presume 100), i.e., at one of the cut-off levels, the p-value was 0.06 for a difference between CCAS and SCAS. Reply: Thank you for this note. We have chosen our best cut-off to be 500, as described in the earlier responses in this document. We have now removed the comparisons that may confuse the reader. We agree that at one of the cut-offs the p-value of 0.06 was boarder line significant, therefore it should be confirmed using a larger sample size in other future studies. Reviewer #2: L361 – the authors indicate here that they have adjusted the methods of the study  in order to maintain statistical significance in their analysis. This is not appropriate. It brings me back to my central concern: that the authors need to justify which cut-off is most appropriate with literature. And if that’s not possible, then maybe a methods paper  is most appropriate for these data.Reply: We agree that our inferences may have not been well spelt out. The comparison of cut-offs was not appropriate for this paper. We will publish such comparisons in a different paper. To avoid any misinterpretations by the reader we have now presented all our data based on the optimum cut-off of 500 as justified in the response to similar comments above. Reviewer #2: L366. Other than limitation of funds, there is not a clear listing of limitations of this study. One of these might be that kappa assumes the two raters are equally competent which is not the case here. Reply: We have now collated our limitations and presented them on L360-366 and L363-370. We present the Kappa and McNemer because they complement each other. Kappa assumes the two raters are equally competent whilst McNemar allows for unequal raters.Attachmentv2Response to reviewers Plos.docxSubmitted filename: Click here for additional data file. 31 Dec 2020PONE-D-20-19224R1Self-collected and clinician-collected anal swabs show modest agreement for HPV genotypingPLOS ONEDear Dr. Dube Mandishora,Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.Please submit your revised manuscript by Feb 14 2021 11:59PM. 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In particular, the policy states that "data points used to create, for example, means and medians, need to be available."[Note: HTML markup is below. Please do not edit.]Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.Reviewer #1: (No Response)Reviewer #2: (No Response)**********2. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: PartlyReviewer #2: Yes**********3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: NoReviewer #2: Yes**********4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.The Reviewer #1: YesReviewer #2: (No Response)**********5. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1: YesReviewer #2: Yes**********6. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1: The authors have satisfactorily addressed all of my previous comments. However, I have some concerns that I had overlooked regarding the statistical analysis, specifically the use of McNamar’s test as a test of agreement (see below). The authors conclude that there is moderate agreement (based on kappa=0.55), but state that this was not statistically significant based on McNamar’s test. However, McNamar’s is a test of proportions, rather than agreement. Thus, the p-value used to support the conclusion is only able to conclude that the proportion of a particular genotype was not significantly different between CCAS and SCAS, rather than indicating agreement. My other comments relate to minor issues that should be easy to address.Abstract: There’s a small typo in conclusions: “with no statistically-significant difference.”Intro:I appreciate the authors’ clarification of the increasing incidence of anal cancer among HIV-infected individuals in the era of ART: “The increase is particularly high among HIV-infectedindividuals regardless of a repaired immune system due to ART, and conversely, extensionto life due to ART tends to give time for cancer to develop [9].” Just to clarify, is the null association at the individual level  or at the ecologic level ? If the latter, I think it may be better to say something like, “The increase is particularly high among HIV-infected individual despite the availability and widespread (?)/ increasing (?) use of ART, which improves individuals’ immunogenic profile. Conversely, ART extends life among HIV infected individuals, giving time for cancer to develop.”Also, please define ART on first use101-103: The last sentence of this paragraph is repeated from above: “Furthermore,patients tend to be more comfortable and less embarrassed when an anal swab is selfcollected [21].112-13: please define SCAS and CCAS on first useMethods:144-148 The information in this paragraph seems redundant with the paragraph below. I suggest omitting this paragraph and integrating any new information provided into the paragraph below.Agreement was tested using kappa and McNamar’s test. However, McNamar’s test compares overall proportions, not agreement :187-191.). I’m not confident that this test can be used to support the authors’ conclusions.Results:Table 3 says CCAS: 124 HPV + samples, SCAS:114 HPV + samples. But paragraph below says 67 and 75, respectively. What is Table 3, last column referring to?249-250: This sentence is confusing and I’m not sure of relevance: In addition, 13/29 of these women had multiple infections in both SCAS and CCAS regardless of HPV genotype and number of infections.Figure 3. I’m confused as to why there’s a single p-value for the McNamar’s test. McNamar’s is used for paired nominal data in a 2x2 contingency table. So, for each genotype CCAS vs. SCAS and genotype present versus genotype absent. It seems like there should be a test statistic and associated p-value for each genotype-comparison, rather than a global McNamar’t test statistic and p-value.Discussion:https://pubmed.ncbi.nlm.nih.gov/30518635/], attributed to vaginal sampling with self-collection versus cervical sampling with CC.327-334: The same has been observed for self-collected versus clinician-collected cervical swabs .” Just to clarify, is the null association at the individual level  or at the ecologic level ? If the latter, I think it may be better to say something like, “The increase is particularly high among HIV-infected individual despite the availability and widespread (?)/ increasing (?) use of ART, which improves individuals’ immunogenic profile. Conversely, ART extends life among HIV infected individuals, giving time for cancer to develop.” Also, please define ART on first use 101-103: The last sentence of this paragraph is repeated from above: “Furthermore, patients tend to be more comfortable and less embarrassed when an anal swab is self-collected [21].Response: Yes, the intention was to explain the latter scenario. The null association is at an ecological level. We have therefore edited the paragraph to include the reviewer’s useful suggestions, L86-88. The acronym ART has now been introduced in L87. The repeated sentence has now been deleted from line 108.Comment 4: 112-13: please define SCAS and CCAS on first useResponse: The acronyms SCAS and CCAS are now introduced on L121, in addition to the definition that was provided in the abstract L40.MethodsComment 5: 144-148 The information in this paragraph seems redundant with the paragraph below. I suggest omitting this paragraph and integrating any new information provided into the paragraph below.Agreement was tested using kappa and McNamar’s test. However, McNamar’s test compares overall proportions, not agreement :187-191.). I’m not confident that this test can be used to support the authors’ conclusions.https://pubmed.ncbi.nlm.nih.gov/10520333/. McNemar is indeed a test of proportion, but the proportion of discordant pairs (ie +/- vs -/+), which gives useful information when evaluating (dis)agreement based on proportions. Indeed, as mentioned by Ranganathan et al, a non-significant McNemar test is not enough to say the agreement is good. It’s however still useful, if interpreted correctly. We have now further clarified our interpretations and limitations in L399-405 of the Discussion section.Response: We agree with the reviewer, stating that agreement was tested using kappa and McNemar can be misleading. To remove this confusion, we have now separated the two statistical analyses to represent (1) measure of agreement (L54-55) and (2) test of proportions (L55). This is also explained in the responses above. The authors believe that both statistical tests are useful. We are also conscious of the fact that there is no perfect test to evaluate agreement and it’s a classical source of debate. Both tests are commonly used together to complement each other ResultsComment 6: Table 3 says CCAS: 124 HPV + samples, SCAS:114 HPV + samples. But paragraph below says 67 and 75, respectively. What is Table 3, last column referring to?Response: We apologise for the misleading column. The 124 and 114 refer to every HPV positivity regardless of multiple infections. In other words, for CCAS, the total read pairs amounted to 124 HPV genotypes in 67 women. This is because some of the 67 women had multiple HPV genotypes, such that there were 32 different HPV genotypes repeatedly detected in 67 women. However, to avoid confusing the reader, the column is now titled “number of HPV positive women”.Comment 7: 249-250: This sentence is confusing and I’m not sure of relevance: In addition, 13/29 of these women had multiple infections in both SCAS and CCAS regardless of HPV genotype and number of infections.Response: We have now removed the statement. Comment 8: Figure 3. I’m confused as to why there’s a single p-value for the McNamar’s test. McNamar’s is used for paired nominal data in a 2x2 contingency table. So, for each genotype CCAS vs. SCAS and genotype present versus genotype absent. It seems like there should be a test statistic and associated p-value for each genotype-comparison, rather than a global McNamar’t test statistic and p-value.Response: The reviewer raises an important question which fortunately we also touched on in the first rebuttal. In our data, each genotype was considered independent because we were most interested in knowing how much HPV was detected in either methods or in comparison. Given the broad array of HPV genotypes that the Illumina sequencer could detect, it was complicated to break down our analyses into each and every HPV genotype. Discordant results were defined as those that were HPV positive on one specimen type while negative on the other. However, we have highlighted this under limitations L294-299 and L371-384. Furthermore, NGS is a highly sensitive assay (DOI:10.1038/s41598-018-36669-6 ) and we do not expect a difference in the capacity for detecting HPV genotypes assuming there are infected cells on the swabs, rather, our research question is whether each collection method harvests enough cells for HPV genotypes to be detected, when comparing two detection methods.Discussionhttps://pubmed.ncbi.nlm.nih.gov/30518635/], attributed to vaginal sampling with self-collection versus cervical sampling with CC.Comment 9: 327-334: The same has been observed for self-collected versus clinician-collected cervical swabs Reviewers' comments:Reviewer's Responses to QuestionsComments to the Author1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.Reviewer #1: (No Response)**********2. Is the manuscript technically sound, and do the data support the conclusions?The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes**********3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes**********4. Have the authors made all data underlying the findings in their manuscript fully available?PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.The Reviewer #1: Yes**********5. Is the manuscript presented in an intelligible fashion and written in standard English?PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.Reviewer #1: Yes**********6. Review Comments to the AuthorPlease use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. Reviewer #1: The authors have fully addressed all of my comments and suggestions. I have a few minor suggestions related to how the kappa and McNemar’s are presented and a few minor edits in the Discussion.Abstract (and throughout) Thank you for clarifying that kappa and McNamar’s were two separate tests used to evaluate concordance. For the sake of clarity, could the following edits be made to the abstract:Methods: Currently: Level of agreement was calculated using the kappa and McNemar tests. Suggested: Level of agreement of HPV genotypes between CCAS and SCAS was calculated using the kappa statistic. McNemar tests were used to evaluate agreement in the proportion of genotypes detected by either method.The same info is available elsewhere in the abstract, but it would improve clarity to include it in the Methods so that readers can better understand the Results.Methods: Similarly, I’d clarify how the statistics were used in the last paragraph of the Methods. Currently: To evaluate agreement of the two collection methods, the McNemar non-parametric test was performed. A kappa test for agreement was also performed to complement the McNemar [38–40]. Suggested: A kappa test was used to evaluate agreement of HPV genotypes across the two collection methods. The McNemar’s non-parametric test was performed to evaluated agreement in the proportion of genotypes detected by either method.Discussion, line 294-300: Current: Based on the moderate level of agreement of HPV genotypes between the two methods, signified by 0.55 in kappa value (k), our data suggest that researchers can use either methods for collection. Furthermore, to evaluate agreement of the methods, McNemar gave a Chi-square value of 0.75 (p=0.39), which showed that the difference in detection rates on the two methods was not statistically significant. Suggested: Based on the moderate level of agreement of HPV genotypes between the two methods, indicated by 0.55 in kappa value (k) and a non-significant test of proportions, our data suggest that researchers can use either methods for collection.Line 351-353 (minor edit): Arbyn et al had similar observations, reporting HPV detection rates 2.28 times higher in self-collected versus clinician-collected vaginal swabs [45].Line 384-389, Current: Indeed, as mentioned by Ranganathan et al, a non-significant McNemar test is not always enough to say the agreement is good. It’s however still useful, if interpreted correctly [51]. In our case, the McNemar is indeed a test of proportion, but the proportion of discordant pairs (ie +/- vs -/+), which gave useful information for evaluating (dis)agreement of HPV genotype detection. Suggested: Indeed, as mentioned by Ranganathan et al, a non-significant McNemar test alone is not sufficient to indicate good agreement. However, it is still a useful statistic, if interpreted correctly [51]. In our case, the McNemar test indicated that the proportion of discordant pairs (ie +/- vs -/+) was not statistically significant, providing useful information for evaluating (dis)agreement of HPV genotype detection.**********what does this mean?). If published, this will include your full peer review and any attached files.7. PLOS authors have the option to publish the peer review history of their article  digital diagnostic tool,  31 Mar 2021Dear Dr Michael ScheurerWe would like to thank you and the reviewers for the additional comments on our work and for the constructive feedback. In the following, we respond to all concerns and comments point-by-point. Review # 1 Comments to the AuthorComment 1: The authors have fully addressed all of my comments and suggestions. I have a few minor suggestions related to how the kappa and McNemar’s are presented and a few minor edits in the Discussion.Abstract (and throughout) Thank you for clarifying that kappa and McNamar’s were two separate tests used to evaluate concordance. For the sake of clarity, could the following edits be made to the abstract:Methods: Currently: Level of agreement was calculated using the kappa and McNemar tests. Suggested: Level of agreement of HPV genotypes between CCAS and SCAS was calculated using the kappa statistic. McNemar tests were used to evaluate agreement in the proportion of genotypes detected by either method.The same info is available elsewhere in the abstract, but it would improve clarity to include it in the Methods so that readers can better understand the Results.Response: We have now included the suggested phrasing on L48-51.Comment 2: Methods: Similarly, I’d clarify how the statistics were used in the last paragraph of the Methods. Currently: To evaluate agreement of the two collection methods, the McNemar non-parametric test was performed. A kappa test for agreement was also performed to complement the McNemar [38–40]. Suggested: A kappa test was used to evaluate agreement of HPV genotypes across the two collection methods. The McNemar’s non-parametric test was performed to evaluated agreement in the proportion of genotypes detected by either method.Response: We have now included the suggested phrasing on L213-216.Comment 3: Discussion, line 294-300: Current: Based on the moderate level of agreement of HPV genotypes between the two methods, signified by 0.55 in kappa value (k), our data suggest that researchers can use either methods for collection. Furthermore, to evaluate agreement of the methods, McNemar gave a Chi-square value of 0.75 (p=0.39), which showed that the difference in detection rates on the two methods was not statistically significant. Suggested: Based on the moderate level of agreement of HPV genotypes between the two methods, indicated by 0.55 in kappa value (k) and a non-significant test of proportions, our data suggest that researchers can use either methods for collection.Response: We have now included the suggested phrasing on L294-297.Comment 4: Line 351-353 (minor edit): Arbyn et al had similar observations, reporting HPV detection rates 2.28 times higher in self-collected versus clinician-collected vaginal swabs [45].Response: We have now added the word “versus” to the sentence, L343-345. Comment 5: Line 384-389, Current: Indeed, as mentioned by Ranganathan et al, a non-significant McNemar test is not always enough to say the agreement is good. It’s however still useful, if interpreted correctly [51]. In our case, the McNemar is indeed a test of proportion, but the proportion of discordant pairs (ie +/- vs -/+), which gave useful information for evaluating (dis)agreement of HPV genotype detection. Suggested: Indeed, as mentioned by Ranganathan et al, a non-significant McNemar test alone is not sufficient to indicate good agreement. However, it is still a useful statistic, if interpreted correctly [51]. In our case, the McNemar test indicated that the proportion of discordant pairs (ie +/- vs -/+) was not statistically significant, providing useful information for evaluating (dis)agreement of HPV genotype detection.Response: We have now rephrased L388-393, to in cooperate the suggestion. Additional edits by authors: Additional information on author contributions has now been included on L428-431, to indicate the unfortunate loss of one of our co-authors BSP, who passed away before the submission of the final version. We have also taken the opportunity to thank the reviewers for their contributions in remoulding this manuscript, L408 specifically mentions Prof. Jane Montealegre and those who also remained anonymous.Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.Reviewer #1: Yes: Jane R MontealegreAttachmentV1_3rd Response to reviewers.docxSubmitted filename: Click here for additional data file. 7 Apr 2021Self-collected and clinician-collected anal swabs show modest agreement for HPV genotypingPONE-D-20-19224R3Dear Dr. Dube Mandishora,We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. 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For more information, please contact Kind regards,Michael Scheurer, Ph.D.Academic EditorPLOS ONEAdditional Editor Comments :Reviewers' comments: 12 Apr 2021PONE-D-20-19224R3  Self-collected and clinician-collected anal swabs show modest agreement for HPV genotyping Dear Dr. Dube Mandishora:I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. onepress@plos.org.If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact plosone@plos.org. If we can help with anything else, please email us at Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staffon behalf ofDr. Michael Scheurer Academic EditorPLOS ONE