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

Preference for sons ans sex ratio in two non-western societies

http://www3.interscience.wiley.com/cgi-bin/jissue/112596548International audienceMoroccan Berbers and the Bolivian Aymara are two unrelated peasant groups living in adverse environments with a still rather traditional agriculture. Precarious life conditions may be responsible for the importance given to male labor and hence for the cultural preference conferred on male descent. This preference, expressed in the social valorization of sons to the detriment of daughters, is more emphasized if the socioeconomic status of the family is lower. Interpreted according to the cost/benefit approach of Fisher ([1958] Genetical Thoery of Natural Selection, New York: Dover) of variations in the sex ratio and to its later developments (Trivers and Willard [1973] Science 179:90–91; Trivers [1985] Social Evolution, Menlo Park: Benjamin/Cummings; Hewlett [1991] J. Anthropol. Res. 47:1–37; Smith [1993] Ethol. Sociobiol. 14:39–44), these cultural characteristics could determine that parents bias the care allocated to their progeny in favor of sons, to the detriment of daughters. This could eventually affect their respective survival and finally modify the offspring tertiary sex ratio. This study compares differences in survival as indicators of parental care according to a child's sex and across three economic strata: poor, medium, and high. The Moroccan data express no other sex differences in survival than an advantage for daughters during the preweaning period in the medium and high strata. Within the same sex and across economic strata, a greater mortality between age 10–20 years is observed for boys of the poorest stratum. The Aymara data do not show sex differences by economic stratum, except for an advantage to daughters between birth and 5 years in the medium group, and no survival differences within the same sex across economic strata. These results suggest either that despite the social valorization of male progeny no differences in parental care according to sex occur, or that their magnitude is not great enough to contrast the survival of sons and daughter

Eaux, pauvreté et crises sociales

Au Nord comme au Sud, l’accès à l’eau, que celle-ci soit à usage domestique ou agricole, devient de plus en plus difficile pour les populations pauvres, alors que les différents types d’exclusion se combinent pour accentuer les inégalités. Pour comparer les processus actuellement en cours sur les cinq continents et tenter d’inverser ces tendances, l’IRD a organisé en 2005 des rencontres à l’université d’Agadir avec l’appui du CRDI et de la Ford Fondation. Les chercheurs, décideurs et responsables d’ONG réunis à cette occasion proposent dans le présent CD un cadre d’action et invitent les pouvoirs publics à renouveler les politiques publiques et répondre aux revendications locales