Seroprevalence of Crimean-Congo hemorrhagic fever virus among people living with HIV in Brazzaville, Congo and among blood donors in Bamako, Mali.

Crimean-Congo hemorrhagic fever virus (CCHFV) is the causative agent of Crimean-Congo hemorrhagic fever (CCHF), a highly contagious and potentially fatal emerging disease. We assessed CCHFV seroprevalence by conducting a serological survey of two cohorts from Brazzaville, Congo and Bamako, Mali. We retrospectively screened 581 sera samples, including 352 from monitoring centers for people living with HIV (PLWH) in Brazzaville and 229 provided by the Blood Transfusion Center at Gabriel Touré Hospital in Bamako. An ELISA kit (ID Screen® CCHF Double Antigen Multi-species, Innovative Diagnostics) was used to detect total anti-CCHFV antibodies in serum. CCHFV seroprevalence was 0.6% in the PLWH cohort in Brazzaville, all in a peri­urban area near livestock/agriculture, and 1.75% in a cohort of blood donors in Bamako, half living in a peri­urban area near livestock/agriculture and the others performing risk-exposure activities, such as working as a butcher or with frequent rural travels. PLWH from Brazzaville were mostly female, older, and more highly educated, with a tertiary sector activity and living in an urban biotope without livestock/agricultural activities in the surroundings, in contrast to the blood donors of Bamako, who were younger and more likely to live in peri­urban/rural areas with livestock/agricultural activities in the surroundings. Despite a low CCHFV seroprevalence, our study indicates human contact with CCHFV in sub-urban areas of the capital cities of Congo and Mali associated with previously described CCHFV risk factors.

Dynamics of SARS-CoV-2 variants characterized during different COVID-19 waves in Mali.

Background: The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants may have contributed to prolonging the pandemic, and increasing morbidity and mortality related to coronavirus disease 2019 (COVID-19). This article describes the dynamics of circulating SARS-CoV-2 variants identified during the different COVID-19 waves in Mali between April and October 2021. Methods: The respiratory SARS-CoV-2 complete spike (S) gene from positive samples was sequenced. Generated sequences were aligned by Variant Reporter v3.0 using the Wuhan-1 strain as the reference. Mutations were noted using the GISAID and Nextclade platforms. Results: Of 16,797 nasopharyngeal swab samples tested, 6.0% (1008/16,797) tested positive for SARS-CoV-2 on quantitative reverse transcription polymerase chain reaction. Of these, 16.07% (162/1008) had a cycle threshold value ≤28 and were amplified and sequenced. The complete S gene sequence was recovered from 80 of 162 (49.8%) samples. Seven distinct variants were identified: Delta (62.5%), Alpha (1.2%), Beta (1.2%), Eta (30.0%), 20B (2.5%), 19B (1.2%) and 20A (1.2%). Conclusions and perspectives: Several SARS-CoV-2 variants were present during the COVID-19 waves in Mali between April and October 2021. The continued emergence of new variants highlights the need to strengthen local real-time sequencing capacity and genomic surveillance for better and coordinated national responses to SARS-CoV-2.

Prevalence of cervical HPV infection, sexually transmitted infections and associated antimicrobial resistance in women attending cervical cancer screening in Mali.

OBJECTIVES: To assess the prevalence of sexually transmitted infections (STIs), antimicrobial resistance and cervical lesions among women from Sikasso, Mali. METHODS: Women infected with human immunodeficiency virus (HIV) (n=44) and HIV-negative women (n=96) attending cervical cancer screening were included. Screening for human papillomavirus (HPV), Chlamydia trachomatis (CT), Mycoplasma genitalium (MG), Neisseria gonorrhoeae (NG) and Trichomonas vaginalis (TV) was performed using polymerase chain reaction assays, and herpes simplex virus (HSV-1/2) serological status was assessed using enzyme-linked immunosorbent assays. Antibiotic resistance tests were performed for MG- and NG-positive cases. RESULTS: A high prevalence of high-risk HPV (hrHPV) infection (63%) was found. This was associated with cervical lesions in 7.5% of cases. An unusual distribution was found, with HPV31, HPV56 and HPV52 being the most prevalent. The hrHPV distribution differed by HIV status, with HIV-positive cases having HPV35/31/51-52-56 and HIV-negative cases having HPV31/56/52. The seroprevalence of HSV-2 was 49%, and the prevalence of other STIs was as follows: CT, 4%; MG, 9%; NG, 1%; and TV, 7%. Five of nine MG-positive specimens and the NG strains obtained were resistant to fluoroquinolone. CONCLUSIONS: These results showed high prevalence of hrHPV and fluoroquinolone resistance in several NG and MG strains. Further studies are required to confirm these data in Mali, and to improve prevention, screening and management of cervical cancer and other STIs in women.

Performance Comparison of Xpert HIV-1 Viral Load Assay and Roche Taqman and Abbott M2000 RT in Bamako, Mali.

BACKGROUND: Routine monitoring of HIV-1 Viral Load (VL) is important in patients on Antiretroviral Therapy (ART) management. Access to HIV VL remains a challenge in resource-limited settings, especially in rural areas. Universal access to VL requires more simplified and less restrictive alternatives to current conventional VL methods. The objective of this study was to evaluate the performance of the new rapid (2-hour turnaround time) Xpert HIV-1VL technique compared to Roche TaqMan and Abbott RT m2000 for HIV-1 RNA quantification in HIV- infected patients. STUDY DESIGN: We conducted a cross-sectional study in patients seen for routine VL monitoring between August and November 2018 in a HIV care site in Bamako. The performance of the Xpert HIV-1 VL assay was evaluated against the Roche TaqMan assay and Abbott m2000 RT assay. Performance, utility and reliability/reproducibility were verified using accuracy, sensitivity, specificity, positive and negative predictive values, Diagnostic Odds Ratio (DOR), Kappa coefficient, Pearson correlation coefficient, and Bland-Altman analysis. RESULTS: The Xpert assay compared well with the two current referral assays (Roche TaqMan and Abbott m2000 RT assays). Compared to Roche TaqMan assay the sensitivity was 93.10%, specificity (97.01%) and accuracy (95.20%), the correlation coefficient of Pearson (r) was 0.98 (p <0.01). Bland-Altman analysis showed a mean difference of 0.18 log10 cp/mL; (Standard Deviation) SD=0.33. Compared to the Abbott m2000 RT, the sensitivity, the specificity and the accuracy were respectively 93.44%; 92% and 92.65%. The Xpert HIV-1 VL assay showed a good correlation with a correlation coefficient of Pearson, r=0.99 (p <0.001). The overall mean difference in the HIV-1 VL values obtained by Xpert HIV-1 VL and Abbott m2000 RT assays was 0.08 log10 cp/mL; SD=0.30. CONCLUSION: Xpert HIV-1 VL showed a good performance compared to Roche TaqMan and Abbott m2000 RT. With the rapid test results (less than 2 h) and ease of testing individual specimens, the Xpert HIV-1 VL assay could be an effective alternative for HIV VL monitoring in resource-limited settings.

Evaluation of Two HIV Rapid Diagnostic Tests in a Context of Strains' Genetic Diversity in Mali.

The rapid diagnostic tests used in most resource-limited countries offer little specificity in the differentiation of HIV-1, HIV-2, and HIV-1 + 2. World Health Organization (WHO) does periodically evaluate rapid tests in use in the South Countries. Despite the prequalification from WHO, it is necessary at local level to conduct comparative studies between the available tests. To do this in Mali, we conducted a cross-sectional study at the University Teaching Hospital Gabriel Touré and the Research and Training Center (SEREFO) of Bamako on 172 samples from retrospective and prospective studies. The goal of this project was to compare the following rapid tests: "HIV TRI-DOT" and OnSite HIV1/2 Ab Plus Combo Rapid Test for screening HIV-1 and HIV-2 to "ImmunoComb II BiSpot" (gold standard). The sensibility and specificity of "HIV TRI-DOT" for HIV-1 detection were 100% each [95% confidence interval (CI): 87.13-100 and 95.31-100]. Its performance for HIV-2 detection was 95.24% (95% CI: 84.21-98.68) (sensibility) and 100% (95% CI: 72.25-100) (specificity). The positive and negative predictive values were, respectively, 100% (95% CI: 91.24-100) and 83.33% (95% CI: 55.20-95.30). The sensibility and specificity of OnSite HIV1/2 Ab Plus Combo Rapid Test assay performance were 100% (95% CI: 87.13-100 and 95.31-100). Overall, OnSite HIV ½ Ab Combo Rapid Test proved to be a good test for warm countries and does not require refrigeration in these settings. Blood and its products can be used to perform the test, unlike "ImmunoComb II BiSpot" and "HIV TRI-DOT," which must be kept cold and cannot be done with whole blood.