Low prevalence of HCV infection with predominance of genotype 4 among HIV patients living in Libreville, Gabon

<div><p>Background</p><p>Gabon is an endemic area for human immunodeficiency virus (HIV) and hepatitis C virus (HCV) and the risk of co-infection is high.</p><p>Method</p><p>Between November 2015 and April 2016, we conducted retrospective study on HCV infection among people living with HIV/AIDS (PLHA). A total of 491 PLHA were included in this study and tested for the presence of HCV infection. HIV viral loads were obtained using the Generic HIV viral Load® assay and the CD4+ T cells count was performed using BD FACSCount™ CD4 reagents. HCV screening was performed using the MP Diagnostics HCV ELISA 4.0 kit. HCV genotypes were determined by sequence analysis of NS5B and Core regions. The Mann-Whitney test was used to compare the groups. Chi-2 test and Fisher's Exact Test were used to compare prevalence.</p><p>Results</p><p>HCV seroprevalence was 2.9% (14/491), (95% confidence interval (CI):1.4–4.3%). The percentage of HCV viremic patients, defined by the detection of HCV RNA in plasma, was 57% (8/14), representing 1.6% of the total population. HCV seroprevalence and replicative infection were not statistically differ with gender. The percentage of co-infection increased with age. No correlation with CD4+ T cells count and HIV viral load level was registered in this study. Identified HCV strains were predominantly of genotype 4 (87.5%) including 4k, 4e, 4g, 4p, 4f and 4c subtypes. Only one strain belonged to genotype 2 (subtype 2q). Analysis of the NS5B region did not reveal the presence of resistance-associated substitutions for sofosbuvir.</p><p>Conclusion</p><p>A systematic screening of hepatitis C is therefore strongly recommended as well as genotyping of HCV strains in order to adapt treatments for the specific case of people living with HIV/AIDS in Central Africa.</p></div

Seroprevalence and HCV RNA by gender, age group, ART treatment, CD4+ T cells and HIV-VL groups.

<p>Seroprevalence and HCV RNA by gender, age group, ART treatment, CD4+ T cells and HIV-VL groups.</p

Phylogenetic analysis of HCV NS5B sequences.

<p>Neighbor-joining phylogenetic tree constructed with our sequences and reference sequences for HCV genotypes retrieved from the GenBank. The Kimura two-parameter method of estimating genetic distance was used. Numbers next to the nodes of the tree represent bootstrap values (1000 replicates). Branches for genotype 4 are indicated in red and in green for genotype 2. Our sequences are preceded by a spot. The Gen-Bank accession numbers of the new NS5b sequences of HCV are KY661744 to KY661751.</p

Characteristics of HIV-HCV co-infected patients.

<p>Characteristics of HIV-HCV co-infected patients.</p

Phylogenetic analysis of HCV Core sequences.

<p>Neighbor-joining phylogenetic tree constructed with our sequences and reference sequences for HCV genotypes retrieved from the Gen-Bank. The Kimura two-parameter method of estimating genetic distance was used. Numbers next to the nodes of the tree represent bootstrap values (1000 replicates). Branches for genotype 4 are indicated in red and in green for genotype 2. Our sequences are preceded by a spot. The Gen-Bank accession numbers of the new core sequences of HCV are KY661736 to KY661743.</p

Seroprevalence and HCV RNA by gender, age group, ART treatment, CD4+ T cells and HIV-VL groups.

<p>Seroprevalence and HCV RNA by gender, age group, ART treatment, CD4+ T cells and HIV-VL groups.</p

Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon

International audienceSince the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa