RESUMO
Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, recombination can only be detected when two genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was simultaneously infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts revealed that Alpha variant alleles comprised between 70-80% of the genomes, whereas the Epsilon variant alleles comprised between 20-30% of the sample. Further investigation revealed the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.
RESUMO
To estimate the level of community exposure to SARS-CoV-2 in Ghana, we conducted phased seroprevalence studies of 2729 participants in selected locations across Ghana. Phase I screening (August 2020) covered a total of 1305 individuals screened at major markets/lorry stations, major shopping malls, hospitals and research institutions involved in COVID-19 work. The screening was performed using a strip-in-cassette lateral flow type Rapid Diagnostic Test (RDT) kit that simultaneously and separately detected IgM and IgG antibodies against SARS-CoV-2 nucleocapsid protein. In Phase I, 252/1305 (19%) tested positive for IgM or IgG or both. Exposure rate was significantly higher among individuals tested at markets/lorry stations (26.9%) compared to those at Shopping Malls (9.4%). The 41-60-years age group had the highest exposure rate (27.2%). People with only a basic level or no formal education had a higher exposure rate (26.2%) than those with tertiary level education (13.1%); and higher in informally employed workers (24.0%) than those in the formal sector (15.0%). Phases II and III screening activities in October and December 2020, respectively, showed no evidence of increased seroprevalence, indicating either a reduced transmission rate or loss of antibody expression in a subset of the participants. The Upper East region has the lowest exposure rate, with only 4 of 200 participants (2%) seropositivity. Phase IV screening in February 2021 showed that exposure rates in the upper income earners (26.2%) had almost doubled since August 2020, reflective of Ghanas second wave of symptomatic COVID-19 cases, which began in December 2020. The Phase IV results suggest that seroprevalence levels have become so high that the initial socioeconomic stratification of exposure has been lost. Overall, the data indicates a much higher COVID-19 seroprevalence in the Greater Accra Region than was officially acknowledged, likely implying a considerably lower case fatality rate than the current national figure of 0.84%. Additionally, the high exposure levels seen in the communities suggest that COVID-19 in Ghana still predominantly presents with none-to-mild symptoms. Our results lay the foundation for more extensive SARS-CoV-2 surveillance in Ghana and the West African sub-region, including deploying rapid antigen test kits in concert to determine the actual infection burden since antibody development lags infection.
RESUMO
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.
RESUMO
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.