Group A human rotaviruses (RVA) are the most common causes of severe viral gastroenteritis in infants and young children worldwide. The available vaccines, while effective in Europe and North America have shown a reduced efficacy in Africa. One issue raised is the genetic variability of RVA. The objective of this study was to perform a literature review of molecular epidemiology to determine the prevalence of RVA genotypes circulating in Africa so as to establish a mapping of reliable data on these various genotypes. The search for articles was done from the National Institutes of Health (PUBMED) using three set of keywords. Articles were selected with inclusion criteria such as the date of publication, the age of the children, the sample size and the diagnostic techniques (standardized laboratory techniques). The data were imported into STATA SE version 11 software. Specific prevalence was estimated with Confidence Intervals (CI) of 95%. A total of 326 published studies were initially retrieved, out of which 27 studies were finally selected for the systematic review. The selected studies cover 20 African countries. The most encountered genotypes in Africa during this period were G1 (32.72%), followed by G2 (17.17%), G3 (9.88%), G9 (8.61%) and G12 (7.56%) among the G-types. The most common P-types were P[8] (48.71%) followed by P[6] (22.60%) and P[4] (11.58%) and the G1P[8] combination (22.64%) was the most encountered followed by G2P[4] (8.29%), G9P[8] (6.95%) and G2P[6] (5.00%). North Africa presented the highest prevalence of the P[8] genotype (65.70%). This review provides a comprehensive view of the current circulating rotavirus strains in Africa, which can be important in light of the new rotavirus vaccinations. Indeed, in Africa, the pursuit of national and continental studies for epidemiological surveillance of circulating rotavirus strains is vital for the promotion of future successful vaccines.

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The vaginal swabs among HIV-positive women in Africa often revealed opportunistic infections such as human Papillomavirus (HPV) and Mycoplasma that induce respectively cervix cancer and diseases such as vaginosis, abortions, infertility in through salpingitis. The purposes of this study were to: (1) seek for, the prevalence of pathogens such as HPV and Mycoplasma; (2) characterize the strains of HPV and estimate their prevalence; (3) identify among these women, those who were co-infected by these pathogens in order to cure them. From February 2009 to January 2010, 156 HIV-positive women attending our medical centers and aged from 19-45 years (mean age 33.65 +/- 5.75 years) had voluntarily accepted vaginal specimen's tests. PCR, ELISA and molecular hybridization were used for the identification and characterization of these pathogens. The results revealed the presence of Mycoplasma and HPV in 25.64 and 58.33% cases, respectively. The following HPV genotypes and the following prevalence were recorded: HPV-50'S (24.11%), HPV-18 (21.28%), HPV-30'S (18.44%) and HPV-16 (5.67%). The study also enable the identification of co-infections such as HPV-18 strains with HPV-30'S (5.67%) and HPV-30'S with HPV-50'S (3.55%). Other germs infecting the female genital tract including Candida albicans (20.51%), Escherichia coli (12.18%), Treponema pallidum (3.85%), Streptococcus agalactiae (3.21%) and Staphylococcus aureus (1.92%) were isolated. This preliminary research work showed the incidence of several genital pathogens, this could be a springboard for nationwide epidemiological study on HPV strains circulating in Burkina Faso.

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This prospective cohort study of 622 women living with human immunodeficiency virus (HIV) from Johannesburg (2012) detected Mycoplasma genitalium in 7.4% (95% confidence interval [CI]: 5.5–9.7, 46/622), with detection more likely with lower CD4 counts(adjusted odds ratio [AOR] 1.02 per 10 cells/μL decrease, 95% CI: 1.00–1.03) and higher plasma HIV-1 RNA (AOR 1.15 per log copies/mL increase, 95% CI: 1.03–1.27). No mutations for macrolide/quinolone resistance was detected.

BackgroundSyphilis continues to be a public health problem, and its diagnosis still has limitations. Molecular diagnosis provides an alternative for rapid and effective management. The objective is to determine the accuracy of tests in the molecular diagnosis of syphilis.MethodsWe searched PubMed and Web of Sciences for articles related to molecular detection of syphilis from January 1, 2009, to December 31, 2019. The bivariate Reitsma model and the hierarchical receiver operating characteristic curve model were used to evaluate the diagnostic performance of molecular tests at a 95% confidence interval. A subgroup meta-analysis was performed to explore sources of heterogeneity.ResultsForty-seven articles were identified for qualitative synthesis, of which 23 met the inclusion criteria for meta-analysis. The pooled sensitivities in conventional polymerase chain reaction (PCR) and real-time PCR were 77.52 (59.50–89.01) and 68.43 (54.96–79.39), respectively. The pooled specificities were 98.00 (90.73–99.59) and 98.84 (97.55–99.46), respectively. Ulcer samples had a better performance (sensitivity of 79.88 [69.00–87.62] and specificity of 98.58 [97.25–99.27]), and the major target genes were the polymerase A gene and tpp47 gene.ConclusionsOur work showed that conventional PCR was more widely used than real-time PCR in the diagnosis of syphilis, and ulcers were the best specimens. Sample types and target genes are factors that may influence the quality of the different tests. These results could provide evidence for further work in the direction of providing a more efficient diagnostic test.

Aims: We aimed at identifying the high-risk HPV genotypes associated with high-grade dysplastic cervical lesions in Burkina Faso. The available vaccines to Burkina Faso only protect against two high risk HPV genotypes: HPV 16 and 18. Are the genotypes identified in the high-grade precancerous lesions in this survey covered by the available vaccines? Methods: The detection and genotyping of high-risk HPV have been conducted based on 118 formalin-fixed and paraffin-embedded archived tissues using the "HPV Genotypes 14 Real-TM Quant" (Sacace biotechnologies ® , Italy) kit allowing for the detection of fourteen high-risk HPV genotypes: HPV 16, 31, 18, 39, 45, 59, 33, 35, 56, 68, 51, 52, 58 and 66. Results: The prevalence of high-risk HPV infections was 48.8% based on the appropriate PCR results (21/43). The most common HPV genotypes were HPV 39 (21.7%), * Corresponding author.C. Ouédraogo et al. 197HPV 35 (13.0%) and HPV 45 (13.0%). Two cases of multiple infections between HPV 39 -45 and HPV 39 -59 have been observed. HPV 16 was not detected in this study. Conclusions: We noted a high prevalence rate for HPV 39, HPV 35 and HPV 45, which are not covered by the commercial vaccines. We also found that the prevalence of HPV 18 was very low in this study and HPV 16 was not detected.