Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks. One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.
The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.
In the absence of an effective vaccine against HIV, it is urgent to develop an effective alternative such as a microbicide. Single and repeated applications of MC1220 microbicide were evaluated in macaques. First, animals were given a single application of 0.5% or 1.5% MC1220-containing liposomal gel. A second group were treated with 0.5% MC1220 once a day for 4 days. The control groups were treated by liposomal gel alone. Thirty minutes after the last application, animals were challenged with RT-SHIV. In the first protocol, 2 of 4 animals treated by 0.5% of the MC1220 and 2 of 5 treated by 1.5% were protected. In the second protocol, 3 of 5 treated animals were protected and 5 of 5 controls were infected. The RNA viral load at necropsy was significantly lower (p=0.05) in treated-infected animals than in controls. In both protocols, the number of CD4+ T cells was lower at viremia peak in infected than in protected animals.
HIV/drug effects , Pyrimidinones/therapeutic use , Reverse Transcriptase Inhibitors/therapeutic use , Simian Acquired Immunodeficiency Syndrome/prevention & control , Simian Immunodeficiency Virus/drug effects , Animals , Antibodies, Viral/blood , Female , Fluorobenzenes , Gels , HIV/genetics , Liposomes , Macaca mulatta , Pyrimidinones/adverse effects , Reassortant Viruses , Reverse Transcriptase Inhibitors/adverse effects , Simian Immunodeficiency Virus/genetics , Viral Load
Human T-cell leukemia virus type 1 (HTLV-1) is highly endemic in areas of central Africa; mother-to-child transmission and sexual transmission are considered to be the predominant routes. To determine the prevalence and subtypes of HTLV-1/2 in pregnant women in Gabon, we conducted an epidemiological survey in the five main cities of the country. In 907 samples, the HTLV-1 seroprevalence was 2.1%, which is lower than that previously reported. Only one case of HTLV-2 infection was found. The HTLV-1 seroprevalence increased with age and differed between regions (P = 0.05), with the highest prevalence (5%) in the southeastern region. A wide range of HTLV-1 proviral loads was observed among the infected women. The level of the proviral load was correlated with a high HTLV-1 antibody titer (P = 0.02). Sequencing of HTLV-1 env and long terminal repeat fragments showed that all but one strain belonged to the central African subtype B; the outlier was of cosmopolitan subtype A. The new strains of subtype B exhibited wide genetic diversity, but there was no evidence of clustering of specific genomes within geographical regions of the country. Some strains were closely related to simian T-cell leukemia virus type 1 strains of great apes, suggesting that in these areas some HTLV-1 strains could arise from relatively recent interspecies transmission. The sole HTLV-2 strain belonged to subtype B. In this study we showed that the prevalence of HTLV-1 in the southeast is one of the highest in the world for pregnant women.
Genetic Variation , HTLV-II Infections/epidemiology , Human T-lymphotropic virus 1/classification , Human T-lymphotropic virus 1/genetics , Human T-lymphotropic virus 2/classification , Human T-lymphotropic virus 2/genetics , Leukemia-Lymphoma, Adult T-Cell/epidemiology , Adolescent , Adult , Cluster Analysis , DNA, Viral/chemistry , DNA, Viral/genetics , Female , Gabon/epidemiology , Genotype , HTLV-II Infections/virology , Human T-lymphotropic virus 1/isolation & purification , Human T-lymphotropic virus 2/isolation & purification , Humans , Leukemia-Lymphoma, Adult T-Cell/virology , Molecular Sequence Data , Phylogeny , Pregnancy , Pregnancy Complications, Infectious , Proviruses/genetics , Proviruses/isolation & purification , Sequence Analysis, DNA , Sequence Homology , Seroepidemiologic Studies , Urban Population , Viral Load