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

Subject marking, object-verb order and focus in Mbuun (Bantu, B87)

In this paper it is demonstrated that the marking of argument focus in Mbuun (B87), a western Bantu language from the Democratic Republic of the Congo (DRC), relies on syntactic and morphological devices that deviate from common tendencies reported in eastern and southern Bantu languages. Focalising a non-verbal constituent in Mbuun obligatorily involves deviations from the canonical SVO order. A focused object is fronted immediately before the verb in Mbuun, resulting in a SOV word order, which runs counter to the narrow focus site immediately after the verb in many other Bantu languages. The object also moves in Mbuun when other non-verbal clause constituents are focused. Both subjects and oblique arguments are focused in situ but their focalisation triggers a movement of the object to clause-initial position resulting in OSV. Morphologically speaking, Mbuun argument focus is peculiar, because it involves a Class 1 a-versus ka-allomorphy in the verbal subject-concord slot, which co-varies not only with focus, but also with tense/aspect. This morphological focus device has not been reported in eastern and southern Bantu, where the so-called 'conjoint/disjoint' distinction in the Tense-Aspect-Mood (TAM) slot is more common. It is, however, a wider western Bantu feature, which may have its origin in an identification copula

Etude morphosyntaxique de la langue mbuun (B87) (parler d’Elyob)

Public defense: 2011-07-11D