Human papillomavirus Genotype Distribution and Co-infection with Sexually Transmitted Pathogens in Reproductive age Women in Urban Gambia

Cervical cancer is the second most common female cancer in The Gambia, and there have been few studies carried out on the causative agent, human papillomavirus (HPV) in this country. The Gambia introduced the quadrivalent HPV vaccine for girls between the ages of 9-13 years in the urban area in 2014; nationwide immunization will take place in 2019. This study determined the common circulating oncogenic HPV types in the urban region where most cervical cancer cases were reported. Two hundred and thirty-two women between 20 – 49 years of age from the urban region who attended a polyclinic were recruited for this work. Endocervical and high vaginal swabs were collected, and a socio-demographic questionnaire was administered to capture potential risk characteristics associated with HPV. Nucleic acid amplification techniques and DNA sequencing were carried out to determine the HPV genotype using PGMY09/11 consensus primers. Phylogenetic analysis was carried out on the Gambian HPV sequences to further confirm the identification of The Gambian HPV genotypes and its relatedness to sequences of the same types from other geographical locations. Microbiological and nucleic acid amplification analyses were used to determine the prevalence of other sexually transmitted pathogens in the participants. Blood samples, endocervical swab, and Pap smear were collected from HIV positive participants and these participants were followed up and re-examined every nine months for 24 months, to determine the persistence of cervical HPV infection, HPV antibodies, and cytological cervical changes. Pseudo-typed neutralisation assays were performed to characterise high-risk HPV antibodies in HIV positive women. Among the sample population studied, HPV prevalence was found to be 12% (28/232). HPV 52 was the most prevalent (17.9%) genotype detected in cervical samples. The Gambian high-risk HPV genotypes, except for a novel putative HPV 35 genotype, were 98 -100% identical to those submitted in the GenBank database. Prolonged (> 5 years) use of hormone contraceptive was the only variable found to associate statistically with HPV infection. Fifty percent (14/28) of participants infected with HPV were co-infected with Ureaplasma urealyticum/parvum and 25% (7/28) with HIV. HPV sero-prevalence was found to be 51.7% (15/29) in HIV positive participants. HIV positive women had been exposed to multiple HPV types and HPV 52 antibody was more prevalent 24% (7/29). Other high-risk HPV genotypes were found to cause high-grade cervical lesions and cancer in HIV positive women. Future studies to investigate oncogenic HPV genotypes in cervical cancer specimens will be useful in providing evidence for policies and future evaluation of the quadrivalent HPV vaccine in The Gambia

Human papilloma virus genotype distribution and risk factor analysis amongst reproductive aged women in urban Gambia

Purpose. Cervical cancer is the most frequently diagnosed female cancer in The Gambia, representing approximately 30% of cases. In 2014, the quadrivalent human papilloma virus (HPV) vaccine was introduced, which offers protection against HPV genotypes 6, 11, 16 and 18. To evaluate the potential effectiveness of this vaccine, genotype distribution and risk factor analysis were assessed. Methodology. Endocervical samples (n=232) were collected from women aged 20-49 years residing in urban Gambia. A questionnaire was administered to capture socio-demographic and cervical cancer risk factors. HPV detection and genotyping was performed by PCR amplification of the L1 major capsid gene and analysis of sequenced PCR products. Results/ Key Findings. The prevalence of HPV was 12% (28/232) and the high risk (HR) genotype HPV 52 (5/28) was the most prevalent genotype. HR-HPV sequences had high identity (≥ 90 %) to isolates which originated from America, Europe and Asia but not from Africa. Half (14/28) of participants were co-infected with Ureaplasma urealyticum/parvum, which increases the risk of progression to cervical cancer. Female genital mutilation and the use of hormone contraception for >5 years were identified as potential risk factors for HPV infection. Ethnicity-associated differences were also noted; participants of the Fula ethnic group had a higher prevalence of HR-HPV infection (31.3%) compared to the Mandinka (18.8%) and Wollof (12.5%) groups. Conclusion. These data may have a significant public health impact as the HPV quadrivalent vaccine may be of limited value if the circulating non-HPV 16/18 HR-genotypes are responsible for cytological abnormalities of the cervix

The effect of live attenuated influenza vaccine on pneumococcal colonisation densities among children aged 24-59 months in The Gambia: a phase 4, open label, randomised, controlled trial.

BACKGROUND: Influenza and other respiratory viruses promote Streptococcus pneumoniae proliferation in the upper respiratory tract. We sought to investigate for what we believe is the first time, the effect of intranasal live attenuated influenza vaccine (LAIV) on nasopharyngeal S pneumoniae density in a low-income to middle-income country population with high pneumococcal carriage rates. METHODS: In an open-label, randomised, controlled trial in The Gambia, 330 healthy children aged 24-59 months were randomly assigned 2:1 to receive one trivalent LAIV dose at enrolment (day 0, intervention) or at the end of active follow-up (day 21, control). The investigator team were initially masked to block size and randomisation sequence to avoid allocation bias. Group allocation was later revealed to the investigator team. The primary outcome was PCR-quantified day 7 and 21 pneumococcal density. Asymptomatic respiratory viral infection at baseline and LAIV strain shedding were included as covariates in generalised mixed-effects models, to assess the effect of LAIV and other variables on pneumococcal densities. The study is registered at ClinicalTrials.gov, NCT02972957, and is closed to recruitment. FINDINGS: Between Feb 8 and April 12, 2017, and Jan 15 and March 28, 2018, of 343 children assessed for eligibility, 213 in the intervention group and 108 in the control group completed the study and were included in the final analysis. Although no significant differences were seen in pneumococcal carriage or density at each timepoint when comparing groups, changes from baseline were observed in the LAIV group. The baseline S pneumoniae carriage prevalence was high in both LAIV and control groups (75%) and increased by day 21 in the LAIV group (85%, p=0·0037), but not in the control group (79%, p=0·44). An increase in pneumococcal density from day 0 amounts was seen in the LAIV group at day 7 (+0·207 log10 copies per μL, SE 0·105, p=0·050) and day 21 (+0·280 log10 copies per μL, SE 0·105, p=0·0082), but not in the control group. Older age was associated with lower pneumococcal density (-0·015 log10 copies per μL, SE 0·005, p=0·0030), with the presence of asymptomatic respiratory viruses at baseline (+0·259 log10 copies per μL, SE 0·097, p=0·017), and greater LAIV shedding at day 7 (+0·380 log10 copies per μL, SE 0·167, p=0·024) associated with higher pneumococcal density. A significant increase in rhinorrhoea was reported in the LAIV group compared with the control group children during the first 7 days of the study (103 [48%] of 213, compared with 25 [23%] of 108, p<0·0001), and between day 7 and 21 (108 [51%] of 213, compared with 28 [26%] of 108, p<0·0001). INTERPRETATION: LAIV was associated with a modest increase in nasopharyngeal pneumococcal carriage and density in the 21 days following vaccination, with the increase in density lower in magnitude than previously described in the UK. This increase was accelerated when LAIV was administered in the presence of pre-existing asymptomatic respiratory viruses, suggesting that nasopharyngeal S pneumoniae proliferation is driven by cumulative mixed-viral co-infections. The effect of LAIV on pneumococcal density is probably similar to other respiratory viral infections in children. Our findings provide reassurance for the use of LAIV to expand influenza vaccine programmes in low-income to middle-income country populations with high pneumococcal carriage. FUNDING: Wellcome Trust

Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks

These authors contributed equally: Alpha K. Keita, Fara R. Koundouno, Martin Faye, Ariane Düx, Julia Hinzmann.International audienc

Evaluation of Convalescent Plasma for Ebola Virus Disease in Guinea

: In the wake of the recent outbreak of Ebola virus disease (EVD) in several African countries, the World Health Organization prioritized the evaluation of treatment with convalescent plasma derived from patients who have recovered from the disease. We evaluated the safety and efficacy of convalescent plasma for the treatment of EVD in Guinea. : In this nonrandomized, comparative study, 99 patients of various ages (including pregnant women) with confirmed EVD received two consecutive transfusions of 200 to 250 ml of ABO-compatible convalescent plasma, with each unit of plasma obtained from a separate convalescent donor. The transfusions were initiated on the day of diagnosis or up to 2 days later. The level of neutralizing antibodies against Ebola virus in the plasma was unknown at the time of administration. The control group was 418 patients who had been treated at the same center during the previous 5 months. The primary outcome was the risk of death during the period from 3 to 16 days after diagnosis with adjustments for age and the baseline cycle-threshold value on polymerase-chain-reaction assay; patients who had died before day 3 were excluded. The clinically important difference was defined as an absolute reduction in mortality of 20 percentage points in the convalescent-plasma group as compared with the control group. : A total of 84 patients who were treated with plasma were included in the primary analysis. At baseline, the convalescent-plasma group had slightly higher cycle-threshold values and a shorter duration of symptoms than did the control group, along with a higher frequency of eye redness and difficulty in swallowing. From day 3 to day 16 after diagnosis, the risk of death was 31% in the convalescent-plasma group and 38% in the control group (risk difference, -7 percentage points; 95% confidence interval [CI], -18 to 4). The difference was reduced after adjustment for age and cycle-threshold value (adjusted risk difference, -3 percentage points; 95% CI, -13 to 8). No serious adverse reactions associated with the use of convalescent plasma were observed. : The transfusion of up to 500 ml of convalescent plasma with unknown levels of neutralizing antibodies in 84 patients with confirmed EVD was not associated with a significant improvement in survival. (Funded by the European Union's Horizon 2020 Research and Innovation Program and others; ClinicalTrials.gov number, NCT02342171.).<br/

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Sexually Transmitted Diseases: Time to Revisit the Syndromic Management Approach

Background: Sexually transmitted disease is a public health challenge especially in resource limited countries. Approximately, 5 million new cases of curable STIs are reported each day, worldwide. The STI syndromic management is widely used in resource limited countries for rapid and same day treatment. The Gambia has adopted the STI syndromic management approach since 1992 and uses a combination treatment of Ciprofloxacin, Doxycycline and Metronidazole for vaginal itching and discharges in females. However, emerging antimicrobial resistance and new identified STI pathogens may pose challenges to the syndromic management approach in the Gambian setting. Study objective: To characterise Ureaplasma and other STI pathogens in women attending an STI clinic who were being treated using the syndromic management approach. Methods: Endocervical (ECS) and high vaginal (HVS) samples were collected from each participants prior treatment (N = 115, Age 20 – 49). Microbiological analysis (Candida, Streptococcus agalactiae, Neisseria gonorrhoeae, T.vaginalis and bacterial vaginosis) and real time PCR (Chlamydia trachomatis, Neisseria gonorrhoeae, Ureaplasma urealyticum/parvum and Mycoplasma genitalium) was carried out. Results: No organism was isolated from 23.5% (27/115) of the participants that reported urogenital symptoms. However, 76.5% (88/115) were infected with either one or more pathogens. The majority 45% (52/115) of participants were infected with urogenital Ureaplasma species either in the cervix, vagina or both. Ureaplasma urealyticum accounts for 19.2 % (10/52), Ureaplasma parvum 80.7% (42/52) and 32.7% (17/52) were co-infected with bacterial vaginosis. Other isolated organisms were: Bacterial vaginosis 29.6% (34/115), Candida albicans 14.8% (17/115), T.vaginalis 13.0% (15/115), Candida species 9.6% (11/115), Streptococcus agalactiae and Neisseria gonorrhoeae each at 6.1% (7/115) were also isolated. Antimicrobial susceptibility profile for Streptococcus agalactiae and Neisseria gonorrhoeae showed resistance to one or more antibiotics used in the first and second line syndromic management treatment. Chlamydia trachomatis and Mycoplasma genitalium was not detected in none of the samples. Conclusion: Confirmation of STI by syndromic management alone is not enough as emerging drug resistance and new STI organisms poses challenges to the health of the reproductive aged woman. There is a need to review the STI syndromic management guidelines and to strengthen laboratory diagnosis to reduce the burden of overuse antibiotic treatment in the Gambia. Treatment of sexual partner(s) should also be encouraged to limit treatment failure and recurrent infection

Prevalance of Ureaplasma parvum and urealyticum in Urban Gambian Women

Urogenital Ureaplasma is associated with urethritis, pelvic inflammatory disease, infertility and adverse pregnancy outcomes in sexually active reproductive aged women. However, it is also frequent in healthy women. The aim of this study was to determine the prevalence and species distribution of Ureaplasma in symptomatic and asymptomatic reproductive aged urban Gambian women (n =179, 20 – 49 years). A questionnaire was administered and endocervical and high vaginal swabs were collected from each participant for the detection of Ureaplasma, Mycoplasma genitalium, Chlamydial trachomatis by real-time PCR, and Trichomonas vaginalis and bacterial vaginosis by microbiological analysis. Ureaplasma was identified in 82 (45.8%) women, of which 45% were symptomatic and 48% asymptomatic. The incidence of Ureaplasma was higher in the 31 – 35 age groups 21 (58.3%). 10% of women who were positive for Ureaplasma were co-infected with T. vaginalis. Bacterial vaginosis was also found in 21% of women with Ureaplasma infection. The most common species in both study groups was Ureaplasma parvum (81.7%). Mycoplasma genitalium and Chlamydial trachomatis were not detected in any of the samples. Risk behaviour analysis shows that 88% of study participants’ partners do not use condom during sexual intercourse. The majority of the study participants reported having one life time sexual partner but are in a polygynous relationship. Bivariate analysis shows that infection with T. vaginalis and using hormone contraceptives for >10 years are risk factors but not significantly associated with Ureaplasma infection (p > 0.05). This is the first study carried out in urban Gambia and it shows that > 40% of sexually active reproductive aged women harbour Ureaplasma either in their cervix, vagina or both, which if left untreated can lead to ascending infection resulting in gynaecological complications

Efficacy Of The Quadrivalent HPV Vaccine In Cervical Cancer Prevention Strategy In The Gambia

Background and Objective: Persistent infection with high risk Human Papillomavirus (HR HPV) genotype causes 80% of cervical cancers. HR HPV 16 and 18 are responsible for 70% of cervical cancer cases, worldwide. Three prophylactic HPV vaccines have been developed to prevent HPV infections. In the Gambia, cervical cancer is the most frequent diagnosed cancer representing approximately 30% of all female cancers. The quadrivalent HPV vaccine, which targets genotypes 16,18, 6 and 11 was recently piloted in the West Coast Region where majority of cervical cancer cases were reported. In order to evaluate the potential efficacy of the quadrivalent vaccine, this study assessed regional genotype distribution to ensure the HPV vaccine prevention strategy would be effective in this population. Methods: 232 endocervical samples were collected from women age 20-49 years old residing in Banjul and West Coast Region. DNA was isolated using the QIAamp DNA Mini Kit (Qiagen). HPV detection was carried out by PCR amplification using primer sets PGMY09/11, which targets the (L1) Major capsid gene of the virus. Genotyping was performed by Sanger sequencing technique. Results: nine different HR- HPV genotypes were identified. HPV 52 (31%) was the most prevalent HR genotype, followed by 51, 58 and 66(each12.5%). HPV 16 accounts for 6% of the HR-HPV and was the eighth of all HPV genotype identified. HR- HPV 18 was not detected in any of the samples. HR-HPV distribution was higher in the 26-30 age group.HPV 61 was the most common low risk genotype isolated. Sequence analysis showed all HR genotypes detected were not homologous to African isolates but isolates that originated from America, Europe and Asia. Conclusion: The success of a cervical cancer vaccine prevention strategy should consider the dominant circulating HR HPV type. In the Gambia, the vaccine currently available may be of limited value if the other HR-HPV types are responsible for cytological abnormalities in these women

A Preliminary Report: Cervical Human Papilloma Virus Genotype Distribution in Reproductive Aged Women Attending Primary Health Care in Urban Gambia

Persistent infection with high risk genotypes of Human Papilloma Virus (HPV) plays a vital role in the development of most cervical cancers and Cervical Intraepithelial Neoplasia (CIN) among sexually active women worldwide. In the Gambia, cervical cancer is the most frequently diagnosed cancer amongst Gambian women representing about 30% of all registered female cancers. The bivalent HPV vaccine, which targets HPV genotypes 16 and 18, was introduced in urban Gambia in 2014. The aim of this study was to determine HPV genotype distribution and the risk factors associated with HPV infections in the urban population and to determine the efficacy of the bivalent vaccine in this population. Sexually active reproductive women (N= 178; 20 - 49 years old) attending a polyclinic were enrolled in the study. A designed questionnaire was administered to capture socio-demographic and behavioural risk factors of study participants. Endocervical and high vaginal swabs were collected to determine HPV genotype distribution and co-infection with other genital STI pathogens. HPV and sample adequacy was determined using the consensus primers PGMY09/11 targeting the late protein (L1) gene and the Histocompatibility leucocyte antigen (HLA) housekeeping gene. HPV genotyping was performed by DNA sequencing on positive HPV samples. Genital STI pathogens were identified by Microbiological analysis and Molecular detection. HPV infection rate was 12.4% and was most prevalence in women between the ages of 31 -39 years old. Overall, 22 HPV genotypes were detected and the most prevalent high risk genotype was HPV 52. About 60% of participants infected with HPV were co-infected with Ureaplasma urealyticum. Bivariate analysis shows that infection with Ureaplasma urealyticum, early sexual debut, Low level of education, female circumcision and having >3 life time sexual partners were all risk factors for HPV infection but not associated significantly with HPV (p > 0.05). This study is the first study carried out in urban Gambia and has demonstrated that the bivalent vaccine might not be adequate to protect this population from HPV infection as most high risk genotypes identified in this study are not targeted by the bivalent vaccine