The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

What is AIDS in Guadeloupe? A descriptive and comparative study.

International audienceSince the pathogen ecology differs between Caribbean regions, specific differences in the most frequent clinical presentations of acquired immunodeficiency syndrome (AIDS) may be expected. We therefore conducted the present retrospective cohort study in order to describe the main AIDS-defining events in Guadeloupe and to compare them with those observed in Metropolitan France and in French Guiana. We discuss the local pathogen ecology, the diagnostic limitations of hospitals in overseas territories and the drivers of the epidemic

Incidence and Risk Factors for Follow-Up Interruption of HIV-Infected Patients in Guadeloupe

International audienceBackground: Guadeloupe is the region of France with the second highest prevalence of HIV. Methods: To determine the risk factors for being lost to follow-up (LFU), a retrospective cohort study of 2,732 patients followed between 1988 and 2009 was conducted, and determined which variables were related to being LFU, i.e. permanently disappearing from HIV clinics or coming back after more than one year of missed appointments. Results: The incidence rate for permanent follow-up interruption was 9 per 100 person-years (8.3-9.7 personyears). The median time of LFU was 6.4 years (interquartile range 3-16.9 years). Cox modelling showed that the younger age groups (HR: 1.60[1.30-2.10], p=0.000) and patients diagnosed before 1997 (HR: 4.80[3.50-6.50], p=0.000) were significantly more likely to be permanently LFU. However, patients treated with HAART had a lower risk of being LFU (HR: 0.63[0.51-0.80], p=0.000). Conclusion: These results suggest that some patients may have died. They also allow to quantify the magnitude of a major yet often under-recognized problem and to identify its predictors in the context of Guadeloupe. This could help clinicians improve patient retention

Sexual risk behaviors and predictors of inconsistent condom use among crack cocaine users in the French overseas territories in the Americas

International audienceThe French overseas territories in the Americas are the French territories most affected by HIV. Crack cocaine users are particularly impacted. The objective of this study was to describe sexual risk behaviors and inconsistent condom use among crack cocaine users. A total of 640 crack cocaine users were interviewed. The sampling method was non-probabilistic. An anonymous standardized questionnaire of 110 questions was used. Over a third of persons did not use condoms systematically with casual sex partners (36.2%) or commercial sex partners (32.3%), and 64% did not use condoms systematically with regular sex partners. In a context of multiple sexual partnerships, frequent forced sex, and insufficient HIV testing, the lack of systematic condom use may favor the spread of HIV. Different predictive factors of inconsistent condom use were identified, depending on the type of partner, with a log binomial regression. However, among the predictor variables identified, two predictive factors frequently occur among the different type of sex partners: high perceived risk of HIV and self-perceived capacity to persuade a sex partner to use condom. These results pointed towards interventions improving access to rights and raising perceived self-efficacy

Comportements sexuels à risque et facteurs prédictifs de non utilisation du préservatif parmi les usagers de crack dans les Départements Français d'Amérique

International audienceRésumé :Introduction : Les départements Français d’Amérique sont à la fois parmi les territoiresfrançais les plus affectés par le VIH et parmi les territoires français les plus impactés par laconsommation de crack. L’épidémie de VIH en Guyane est une épidémie concentrée quitouche plus spécifiquement certains groupes vulnérables. Parmi ces groupes, les usagers decrack sont particulièrement touchés.Matériel et Méthodes : Une étude a été réalisée simultanément dans les trois départements en2012 dans le but de décrire les connaissances, les attitudes et les pratiques vis-à-vis du VIH etdes IST chez les usagers de crack. Au total 640 personnes ont été interrogées. La méthoded’échantillonnage utilisée était non probabiliste et combinait un échantillonnage deconvenance dans les associations recevant ce public (75% de l’échantillon), et unéchantillonnage en boule de neige en dehors afin d’atteindre les personnes ne fréquentant pasles structures (25% de l’échantillon).Résultats : Un tiers des personnes n’utilisait pas systématiquement le préservatif avec lespartenaires occasionnels (36,2%) ou avec les partenaires commerciaux (32,3%), et 64%n’utilisaient pas le préservatif à chaque fois avec les partenaires réguliers. Différents facteursprédictifs de la non utilisation du préservatif ont été identifiés selon le type de partenaire àl’aide d’un modèle log-binomial. Parmi les différents facteurs repérés, deux étaient communsà chaque type de partenaire : la perception élevée de son risque face au VIH et le fait de nepas se sentir à l’aise pour persuader un partenaire à utiliser le préservatif.Discussion : Dans un contexte de multipartenariat, de violences sexuelles fréquentes et dedépistage insuffisant du VIH, la non utilisation systématique du préservatif peut avoir unimpact non négligeable dans la diffusion de l’épidémie. Bien que la non utilisation dupréservatif soit sensiblement inférieure à ce que l’on retrouve dans la littérature, cesproportions traduisent un réel problème.La capacité à persuader un partenaire sexuel à utiliser un préservatif était négativementcorrélée avec la non utilisation du préservatif quel que soit le type de partenaire. Ainsi, ilsemble que lorsque les personnes se sentaient capables de négocier l'utilisation du préservatif,elles l’utilisaient de manière plus systématique. La capacité personnelle perçue est souventconsidérée comme un levier important pour adapter les comportements de santé. Or, elle peutêtre affectée dans des situations de stigmatisation, d’addiction ou de relation violente. Cesrésultats soulignent l’importance d’interventions spécifiques de prévention parmi les usagersde crack et notamment des interventions visant à améliorer le sentiment d’efficacitépersonnelle (perceived self-efficacy) et d’estime de soi

Sexual risk behaviors and predictors of inconsistent condom use among crack cocaine users in the French overseas territories in the Americas

International audienceThe French overseas territories in the Americas are the French territories most affected by HIV. Crack cocaine users are particularly impacted. The objective of this study was to describe sexual risk behaviors and inconsistent condom use among crack cocaine users. A total of 640 crack cocaine users were interviewed. The sampling method was non-probabilistic. An anonymous standardized questionnaire of 110 questions was used. Over a third of persons did not use condoms systematically with casual sex partners (36.2%) or commercial sex partners (32.3%), and 64% did not use condoms systematically with regular sex partners. In a context of multiple sexual partnerships, frequent forced sex, and insufficient HIV testing, the lack of systematic condom use may favor the spread of HIV. Different predictive factors of inconsistent condom use were identified, depending on the type of partner, with a log binomial regression. However, among the predictor variables identified, two predictive factors frequently occur among the different type of sex partners: high perceived risk of HIV and self-perceived capacity to persuade a sex partner to use condom. These results pointed towards interventions improving access to rights and raising perceived self-efficacy

Transactional sex among men who have sex with men in the French Antilles and French Guiana: frequency and associated factors

International audienceThe French Antilles (Martinique, Saint Martin and Guadeloupe) and French Guiana are the French territories most affected by the HIV epidemic. Some population groups such as men who have sex with men (MSM), especially those involved in transactional sex, are thought to be particularly vulnerable to HIV but few data exist to help characterize their health-related needs and thus implement relevant prevention interventions. To fill this knowledge gap, we used data collected from an HIV/AIDS Knowledge, Attitudes, Behaviours and Practices survey conducted in 2012 among MSM living in the French Antilles and French Guiana and recruited through snowball sampling. Our objectives were to compare social and demographic characteristics and sexual behaviours between MSM engaging in transactional sex and MSM not engaging in transactional sex and to identify factors associated with transactional sex involvement using a logistic regression model. A total of 733 MSM were interviewed, 21% of whom reported to undergo transactional sex. Their behaviour and social and demographic characteristics were different from other MSMs’ and they were more exposed to factors that are recognized to potentiate HIVvulnerability, at the individual, community, network and structural levels. The variables positively associated with sex trade involvement were having ever consumed drug (OR = 2.84 [1.23–6.52]; p = .002), having a greater number of sex partners than the median (OR = 8.31 [4.84–14.30]; p < .001), having experienced intimate partner violence (OR = 1.72 [0.99–3.00]; p = .053) and having undergone physical aggression because of sexual orientation (OR = 2.84 [1.23–6.52];p = .014). Variables negatively associated with sex trade involvement were being older (OR = 0.93 [0.90–0.97] per year; p = .001), having a stable administrative situation (OR = 0.10 [0.06–0.19]; p < .001), having a stable housing (OR = 0.29 [0.15–0.55]; p < .001) and being employed full-time (OR = 0.29 [1.23–6.52]; p = .002)

Genre et développement

Rassembler ces huit communications en une brochure n'a rien d'artificiel. On s'aperçoit en effet qu'elles suivent un fil conducteur évident. Non seulement elles se rassemblent autour d'un thème "genre et développement", mais surtout, elles s'enchaînent l'une l'autre dans une suite parfaitement logique. Le dossier s'ouvre par la synthèse présentée par Thérèse Locoh de l'ensemble des travaux des trois ateliers organisés sur le genre dans le cadre du colloque. Vient ensuite une réflexion sur le thème lui-même. Après quoi les six communications suivantes déclinent le même thème à différentes étapes de la vie : le choix du conjoint, le mariage, la fécondité, le confiage des enfants et la migration

Intimate partner violence by men living with HIV in Cameroon: Prevalence, associated factors and implications for HIV transmission risk (ANRS-12288 EVOLCAM)

International audienceObjectives: Intimate partner violence (IPV) against women is frequent in Central Africa and may be a HIV infection risk factor. More data on HIV-positive men (MLHIV) committing IPV are needed to develop perpetrator-focused IPV and HIV prevention interventions. We investigated the relationship between IPV and HIV transmission risk and IPV-associated factors.Methods: We used data from the cross-sectional survey EVOLCam which was conducted in Cameroonian outpatient HIV structures in 2014. The study population comprised MLHIV declaring at least one sexual partner in the previous year. Using principal component analysis, we built three variables measuring, respectively, self-reported MLHIV-perpetrated psychological and physical IPV (PPV), severe physical IPV (SPV), and sexual IPV (SV). Ordinal logistic regressions helped investigate: i) the relationship between HIV transmission risk (defined as unstable aviremia and inconsistent condom use) and IPV variables, ii) factors associated with each IPV variable.Results: PPV, SPV and SV were self-reported by 28, 15 and 11% of the 406 study participants, respectively. IPV perpetrators had a significantly higher risk of transmitting HIV than non-IPV perpetrators. Factors independently associated with IPV variables were: i) socio-demographic, economic and dyadic factors, including younger age (PPV and SPV), lower income (PPV), not being the household head (SPV and SV), living with a main partner (SPV), and having a younger main partner (SPV); ii) sexual behaviors, including ≥2 partners in the previous year (PPV and SPV), lifetime sex with another man (SPV), inconsistent condom use (SV), and >20 partners during lifetime (SV); iii) HIV-related stigma (PPV and SV).Conclusion: IPV perpetrators had a higher risk of transmitting HIV and having lifetime and recent risky sexual behaviors. Perpetrating IPV was more frequent in those with socioeconomic vulnerability and self-perceived HIV-related stigma. These findings highlight the need for interventions to prevent IPV by MLHIV and related HIV transmission to their(s) partner(s)