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This is the supplementary information of the manuscript entitled, "Molecular identification of cervical microbes in HIV-negative and HIV-positive women in an African setting using a customized Bacterial Vaginosis Microbial DNA qPCR Array" - https://doi.org/10.6084/m9.figshare.19714483. The supplementary information contains the following two files: TABLE S1 Distribution of the baseline characteristics of the women according to their age group. FIG S1 Cumulative prevalence of STI/pathobiont, individual STIs, and individual pathobionts according to age category of women with normal cervical cytology.

Patterns of bacterial pathobiont infections according to vaginal HPV status among 192 AGYW. HPV-positive AGYW with (a) single infections, (b) dual infections, (c) triple infections; and HPV-negative AGYW with (d) single infections, (e) dual infections, (f) triple infections. The number of AGYW in each group is in parentheses. Of all the AGYW with information on HPV status, 193 had any detectable pathobiont (M. genitalium, M. hominis, U. parvum, or U. urealyticum). One HPV-positive participant, not included in any of the two-dimensional pie charts showing the patterns of infections, had all the four examined pathobionts detected.

Background This study investigated the prevalence of HPVs in heterosexual South African men and the impact of HIV co-infection. Methods HPV was detected in penile swabs from 195 HIV-infected and 140 HIV-uninfected men using PCR with FAP59/64 primers and Roche Linear Array HPV genotyping (LA). Genotyping of FAP positive specimens was achieved by high-throughput sequencing of amplicons. Results HPV was detected by FAP PCR and LA in 79% (266/335) of the men. Men with HIV co-infection and men with HIV infected sexual partners had a significantly (p

This study constitutes the first report on type-specific human papillomavirus (HPV) concordance and transmission in heterosexually active couples that are human immunodeficiency (HIV)-seronegative, HIV-seropositive or HIV-discordant and in which 71% of female participants have normal cervical cytology.

Objectives HPV infection causes cervical cancer, yet information on prevalence and risk factors for HPV in Africa remain sparse. This study describes the prevalence of HPV genotypes and risk factors associated with HPV among young women ≤ 30 years of age in KwaZulu-Natal (KZN), South Africa. Methods Cervicovaginal lavage samples were tested for HPV genotypes in 224 women enrolled in a prospective cohort study. Clinical, behavioural and demographic data were collected. We measured prevalence of HPV genotypes and using logistic regression, examined for factors associated with HPV. Results Median age of participants was 21 years [interquartile range (IQR):18–23]. The overall prevalence of HPV was 76.3% (171/224) with multiple and single genotypes prevalent in 56.3% and 20.1% of women respectively. Proportion of women with high-risk genotypes (16, 18, 31, 33, 35, 39, 45, 51, 52, 56 and 58) was 54.5%. Women not living with their partner [adjusted odds ratio (aOR)] = 3.42 95% CI1.22–9.60; p = 0.019), was significantly associated with HPV infection and high-risk HPV genotype infection. Conclusion The high burden of HPV and associated risk behaviours highlight the need to intensify behavioural interventions to prevent HPV acquisition in young women. The large scale delivery of HPV vaccine should be prioritised to prevent HPV acquisition and reduce HPV-related morbidity.

Introduction: Human papillomavirus (HPV) infection is an important public health problem facing black African women. Persistent infection with high-risk (HR) HPV types is the key factor for the development of cervical cancer. Coinfection of HPV with other sexually transmitted pathogens contributes to the progression of cervical cancer. Preventative measures including screening for and treating pre-cancerous cervical lesions as well as HPV vaccination have been implemented in parts of South Africa. However, in the rural Eastern Cape Province there is limited information on the prevalence of HPV and the HPV types associated with cervical lesions. Two cohorts were chosen to study HPV in the Eastern Cape (South Africa), a community clinic, and a referral hospital for treatment of cervical lesions. This study aimed at determining the prevalence of HPV, risk factors of HPV, coinfection of HPV with sexually transmitted pathogens and evaluate the performance of a number of HPV tests for HPV detection and cervical cancer screening. The objectives of the study were: • To investigate the prevalence of HR-HPV and factors associated with HR-HPV infection among women from rural Eastern Cape, South Africa. • To investigate the distribution of HPV genotypes among women with cervical intraepithelial lesions according to HIV status from Eastern Cape Province, South Africa. • To investigate HR-HPV prevalence and compare agreement between cliniciancollected and self-collected genital specimens as well as two different HPV tests on clinician-collected samples. • To investigate the prevalence of sexually transmitted pathogens and co-infection of with HR-HPV infection among women from rural Eastern Cape Province, South Africa. Methods: A total of 741 participants were recruited from the Mbekweni Community Clinic (N=417) and the Nelson Mandela Hospital Referral Clinic (N=324) located in the OR Tambo municipality of the Eastern Cape Province. Clinician-collected cervical scrapes from women attending the Community Clinic were screened for HR-HPV prevalence and HR-HPV viral load using Hybrid Capture 2 (HC-2, Qiagen Inc., Gaithersburg, MD; USA); Cervical clinician-collected and vaginal self-collected specimens of women with or without abnormal cytology from both study cohorts were also screened for HR-HPV infection using hpVIR real-time PCR. HPV typing of clinician-collected cervical specimens from women with cervical intraepithelial neoplasia grades 2 and 3 (CIN 2 / 3) was done using Direct Flow Chip HPV kit (Master Diagnostica, Spain). Cervical specimens from the Community Clinic (N=205) were also tested for sexually transmitted infections (STIs) namely Chlamydia trachomatis: CT, Haemophilus ducreyi, Herpes Simplex Virus type 2, Neisseria gonorrhoeae: NG, Treponema pallidum, and Trichomonas vaginalis: TV) and pathobionts (Ureaplasma spp: (UP), Mycoplasma genitalium: MG, and Mycoplasma hominis: MH) using the STD Direct Flow Chip kit (Master Diagnostica, Spain). The univariate and multivariate analysis was used to determine the correlation between HPV infection and potential behavioural risk factors using STATA 14.2 (Stata Corp, College Station, Texas). A chi squared test was used determine the difference in estimated HR-HPV prevalence between self-collected and clinician-collected samples. STIs prevalence and association with behavioural risk factors were analysed using GraphPad Prism v6.01 (GraphPad Software, Inc., San Diego, CA). Results: Of the 417 women from the community clinic, HR-HPV prevalence was significantly higher in HIV-positive women compared to HIV-negative women (40.6%, 63/155 vs 21.4%, 56/262, p< 0.0001). Among women referred to Nelson Mandela Hospital with cervical intraepithelial lesions, HPV prevalence was observed to be significantly higher in HIV-positive than HIV-positive women (98.0% vs 89.1%, p=0.012). Similarly, HIV-positive women (65.3%, 96/147) had higher multiple HPV infections than HIV-negative women (47.8%, 22/46; p=0.034). HPV35 (23.9%), HPV58 (23.9%), HPV45 (19.6%), and HPV16 (17.3%) were the most frequently detected HPV types in CIN2, while HPV35 (22.5%), HPV16 (21.8%), HPV33 (15.6%), HPV58 (14.3%) were commonly detected in women with CIN3 regardless of HIV status. HR-HPV prevalence in clinician-collected samples was equivalent to self-collected samples from both study sites, the community clinic (26.4% vs 27.9%, p=0.601) and the referral clinic (83.6% vs 79.9%, p=0.222). HR-HPV positivity between self-collected and clinician-collected samples showed an agreement of 86.9% for community clinic (k=0.669) and 91.4% for referral clinic (k=0.711). The distribution of HR-HPV genotypes was similar between self-collected and clinician-collected samples from both study sites. The agreement of HR-HPV genotypes between self-collected and clinician ranged from moderate to almost perfect (0.571-0.888). A majority of women reported a high positive response of acceptance for self-collection (community-based clinic: 77.2% and referral clinic: 83.0%). HR-HPV detection agreement between hpVIR real-time PCR and HC-2 was almost perfect (87.7%, k=0.754). The prevalence of the six traditional STIs (CT, TV, NG, HSV-2, TP, and Haemophilus ducreyi) was high (22.9%, 47/205). TV was the most frequently detected STI (15.6%, 32/205). UP (70.2%, 144/205) and MH (36.6%, 47/205) were the most frequently identified pathobionts. Multiple infections/coinfections with more than two STIs/pathobionts was found in 52.7% (108/205) of women with UP/MH (26.9%) and UP/HPV (21.3%) the frequently identified coinfections. HR-HPV infection was significantly associated with HIV infection (p=0.017) and HSV-2 (p=0.026). Conclusion: This study shows that HIV infection and sexual behaviour increased the risk of HPV infection among women from the community clinic. HIV-positive women had significantly higher HPV viral load and multiple HPV type infections compared with HIV-negative women with or without cervical lesions. Since HIV positive women are at higher risk of HPV infection they need to continue to be screened more regularly for cervical lesions and treated when appropriate. In addition, the high prevalence of HPV in the community of HIV negative women indicates that a robust cervical screening programme is needed to implement the cervical screening policy of South Africa. Thus, the women get the allocated three cervical smears in a life time. Distribution of HPV types was similar among women with CIN2 & 3 with HPV35 being the most frequently detected HPV type regardless of HIV status. This highlights the importance for the inclusion of HPV-35 in the next generation of HPV prophylactic vaccines. The findings of this study add to the limited information on genital HPV infection in women from this province. Moreover, our data now acts as a baseline/reference data for future investigations. The data will also contribute to discussions on HPV testing as the primary screening strategy for cervical cancer and HPV vaccination in South Africa. The hpVIR real-time PCR test between self-collected and clinician-collected specimens showed comparable agreement for the detection of HPV infection. The type-specific concordance between self-collected and clinician-collected showed moderate to an excellent agreement, indicating that self-collection can be utilised as the alternative screening tool for cervical cancer. The participants showed a high positive response for the self-collection method, indicating that introducing this method can positively impact the cervical cancer screening program. However, hpVIR real-time PCR is an in-house test which is not practical to introduce on a large scale in South Africa. Therefore, future research should be done to determine what other HPV tests could be done on these types of specimens. Presently, syndromic management is used to treat STI at clinics in South Africa. The high prevalence of sexually transmitted pathogens necessitates the need to enhance the current screening methods for these pathogens.