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

Caratterizzazione e valorizzazione genetica della razza bovina autoctona Varzese

La presente ricerca \ue8 finalizzata a supportare ed integrare le informazioni oggi disponibili sui soggetti di razza Varzese - Ottonese - Tortonese attraverso l\u2019identificazione dei soggetti stessi ed una prima analisi della distanza genetica tra essi per creare le basi operative di un successivo progetto integrato di valorizzazione della biodiversit\ue0 e salvaguardia della razza. La variabilit\ue0 genetica. Fino ad oggi con un pannello internazionalmente riconosciuto di marcatori del DNA genomico (microsatelliti) \ue8 stata caratterizzata gran parte della popolazione esistente distribuita nelle diverse provincie: 65 femmine e 9 maschi, oltre a paillettes di seme, ancora ad alto potere fecondante, differenziabili unicamente dal colore e successivamente identificate come appartenenti a 8 soggetti prelevati negli anni \u201880. I dati molecolari indicano che la maggior parte degli alleli si sono conservati nel tempo, cos\uec come l\u2019eterozigosi, con un leggero aumento del numero degli alleli nella popolazione attuale, dovuto in parte alla pi\uf9 estesa campionatura. La popolazione attuale pur non essendo in equilibrio di Hardy Weinberg, come ci si attende dopo un collo di bottiglia quale quello verificatosi negli scorsi decenni e in una popolazione sottoposta a selezione, presenta comunque una variabilit\ue0 significativamente alta (FWC(IS)=-0.011; Genepop v.3.4)., I campioni di seme degli anni \u201980 sono invece in equilibrio e possono essere considerati perci\uf2 una campionatura corretta e indicativa, anche se parziale, della pi\uf9 vasta popolazione del recente passato. Se si considerano le sottopopolazioni maschile e femminile come genotipi individuali (Genetix v 4.03, Analisi delle Componenti Principali), circa met\ue0 dei maschi (prevalentemente costituiti da seme della vecchia popolazione) si aggregano separatamente rispetto alle femmine. Le vecchie paillettes quindi, che forniscono un quadro parziale ma rappresentativo della variabilit\ue0 pregressa, costituiscono un\u2019ottima riserva genetica cui attingere per la rinascita della razza

Characterization of bovine TGM1 and exclusion as candidate gene for ichthyosis in Chianina

Ichthyosis is a heterogeneous group of keratinisation disorders reported both in human and animals. Two inherited forms have been reported in cattle, both characterised by autosomal recessive transmission. Ichthyosis reports in cattle is quite rare and the disease genetic basis are completely unknown. In order to find the causative mutation TGM1 gene was evaluated as candidate gene by comparison with man, where the gene is very frequently associated to autosomal recessive ichthyosis forms. TGM1 was characterised in bovine and three different polymorphisms were identified in 5’end region. 2 microsatellite marker polymorphisms saturating about 10cM in the flanking Bovine TGM1 orthologous region were also considered. No gene mutation as well as marker homozygosity were shown in affected calves. Statistical analysis significantly excluded TGM1 gene as causative for ichthyosis phenotype in the analyzed Chianina cases