Interest of seroprevalence surveys for the epidemiological surveillance of the SARS-CoV-2 pandemic in African populations: insights from the ARIACOV Project in Benin

BackgroundMany SARS-CoV-2 seroprevalence surveys since the end of 2020 have disqualified the first misconception that Africa had been spared by the pandemic. Through the analysis of three SARS-CoV-2 seroprevalence surveys carried out in Benin as part of the ARIACOV project, we argue that the integration of epidemiological serosurveillance of the SARS-COV2 infection in the national surveillance package would be of great use to refine the understanding of the COVID-19 pandemic in Africa. MethodsThree repeated cross-sectional surveys have been carried out in Benin, two in Cotonou, the economic capital in March and May 2021, and one in Natitingou, a semi-rural city in North in August 2021. The global and by age-groups weighted seroprevalences have been estimated and the risk factors of the infection by SARS-COV-2 have been assessed by using logistic regression. ResultsIn Cotonou, a slight increase in overall age-standardized SARS-CoV-2 seroprevalence from 29.77% (95% CI: 23.12-37.41%) at the first survey to 34.86% (95% CI: 31.57-38.30%) at the second survey was observed. In Natitingou the global adjusted seroprevalence was 33.34% (95% CI: 27.75-39.44%), much higher than expected. Adults over 40 seemed to be more at risk than the youngest during the first survey in Cotonou but no longer in the second survey, showing the persistence of the SARS-COV-2 virus circulation outside the epidemic waves. ConclusionsA routine serological surveillance on strategic sentinel sites and / or populations could constitute a cost / effective compromise to better anticipate the onset of new waves and define public health strategies.

High Prevalences and a Wide Genetic Diversity of Simian Retroviruses in Non-human Primate Bushmeat in Rural Areas of the Democratic Republic of Congo.

Like the majority of emerging infectious diseases, HIV and HTLV are of zoonotic origin. Here we assess the risk of cross-species transmissions of their simian counterparts, SIV and STLV, from non-human primates (NHP) to humans in the Democratic Republic of Congo (DRC). A total of 331 samples, derived from NHP bushmeat, were collected as dried blood spots (DBS, n = 283) or as tissue samples (n = 36) at remote forest sites mainly in northern and eastern DRC. SIV antibody prevalences in DBS were estimated with a novel high throughput immunoassay with antigens representing the actual known diversity of HIV/SIV lineages. Antibody-positive samples were confirmed by PCR and sequence analysis. Screening for STLV infection was done with universal primers in tax, and new strains were further characterized in LTR. SIV and STLV infection in tissue samples was done by PCR only. Overall, 5 and 15.4% of NHP bushmeat was infected with SIV and STLV, respectively. A new SIV lineage was identified in Allen's swamp monkeys (Allenopithecus nigroviridis). Three new STLV-1 subtypes were identified in Allen's swamp monkeys (Allenopithecus nigroviridis), blue monkeys (Cercopithecus mitis), red-tailed guenons (Cercopithecus ascanius schmidti) and agile mangabeys (Cercocebus agilis). SIV and STLV prevalences varied according to species and geographic region. Our study illustrates clearly, even on a small sample size from a limited number of geographic areas, that our knowledge on the genetic diversity and geographic distribution of simian retroviruses is still limited and that humans continue to be exposed to relative high proportions on infected NHP bushmeat.

Modeling CD4+ cell count increase over a six-year period in HIV-1-infected patients on highly active antiretroviral therapy in Senegal.

To assess the extents and determinants of long-term CD4 cell increases after initiation of antiretroviral therapy (ART), changes in CD4 cell counts were analyzed in a cohort of HIV-1-infected Senegalese using a mixed-effects model. After a median follow-up of 54 months, an average of 483 CD4 cells/mm3 (95% confidence interval [CI] = 331; 680) was reached. The average asymptote level was approximately 421 cells/mm3 (95% CI = 390; 454) in patients with < 200 cells/mm3 at baseline and approximately 500 cells/mm3 in patients with > 200 cells/mm3. The independent predictors of long-term CD4 cell reconstitution were the baseline CD4 cell count and the monthly average viral load over the entire follow-up. This good long-term immune reconstitution, optimal in subjects with low average viral loads and > 200 CD4 cells/mm3 at baseline, argues in favor of the earliest possible access to ART and underlines the importance of strict compliance with the treatment.

Genetic characterization of HIV-1 strains in Togo reveals a high genetic complexity and genotypic drug-resistance mutations in ARV naive patients.

In this study, the genetic diversity of HIV-1 and the presence of genotypic drug-resistance mutations in ARV naive patients in Lomé, the capital city of Togo, was documented for the first time. Between June 2006 and January 2007, 83 plasma samples were collected in Lomé from HIV-1 positive and antiretroviral (ARV) naive individuals. Pol (protease+RT) and env (V3-V5) regions were amplified and sequenced. Phylogenetic and recombination analyses were done to identify the HIV-1 variants. Pol sequences were then inspected to identify presence of drug-resistance mutations based on the WHO list recommended for epidemiological studies. A total of 75 plasma samples were amplified and sequenced in both genomic regions. The phylogenetic analysis showed that CRF02 (48.7% and 51.2%) and G (12.8% and 16.2%) were predominant, followed by A3 (6.4% and 6.2%) and CRF06 (3.8% and 12.5%) in pol and env, respectively. One strain was identified as CRF05 in pol and env. Two divergent subtype A strains in env were undetermined (U) in pol but clustered with a previously described complex recombinant strain, 99GR303. Overall, at least 23/83 (27.7%) strains were recombinant, 19 had a unique recombinant structure in pol, and 4 had discordant subtype/CRF designations between pol and env. The subtypes/CRFs involved in the recombination events corresponded to those already circulating as non-recombinant strains in the country. A total of 8 patients harbored strains with mutations associated to drug resistance: L90M (n=1), K103N (n=1), T69N (n=1), T215S (n=1), M41L (n=4). In this study we showed the complexity of the HIV-1 strains circulating in Togo and documented a relative high proportion of ARV naive patients with drug-resistance mutations. The high number of resistant strains observed in Togo needs further attention and additional studies are needed to confirm this trend especially because the national ART program experienced major problems to provide drugs on a regular base.

Short and Long-Term Incidence of Tuberculosis and CD4-Cell Count Dynamic on HAART in Senegal.

OBJECTIVES: Estimate tuberculosis (TB) incidence among patients receiving HAART. Compare the dynamic of the CD4-cell count and viral load before notification of the TB with the dynamic among patients remaining free of TB. DESIGN: Prospective cohort with ascertainment of TB cases from medical records. METHODS: The first 404 adults HIV-1 infected patients enrolled in the Senegalese antiretroviral drug access initiative were eligible. CD4-cell and viral load were assessed at baseline and every 6 months. Patients receiving an antituberculosis treatment at HAART initiation were excluded from analysis. Any TB case notified after the first month of HAART was considered as an incident case. Follow-up was censored at death or at the last visit before March 31, 2008. CD4-cell trajectories until TB notification were compared to non-TB developers within two distinct periods: from HAART initiation to 24 months and after. RESULTS: Over 404 eligible patients, 352 were included in this analysis. Median follow-up reached 73 months and 1821 person-years were accrued. Half of the 42 incident cases were notified before month 19 of HAART yielding to an overall incident rate of 2.3/100 PY [1.7-3.1]. Annual incidence decreased with duration of HAART (trend in incidence: RR=0.26, p<10(-4)). During the first period, CD4-cell count dynamic of most TB patients was identical to the dynamic among patients remaining free of TB. Most cases of the second period occurred in a context of an immunological failure. CONCLUSIONS: This study provides an estimate of TB incidence among patients on HAART in Senegal and supports two underlying mechanisms.