RESUMO
Serological assays for detection of IgG, IgM or IgA against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) play an important role in surveillance, antibody persistence, vaccine coverage and infection rate. Serological assays, including both ELISA and rapid lateral flow assays, are available commercially but the cost limits their accessibility for low resource countries. Although serological assays based on mammalian-expressed SARS-CoV-2 spike protein have been previously described these assays need to be validated using samples from local populations within the continent, or country, in which they will be used. Interpretation of results could be influenced by differences in specificity and potential for pre-existing cross-reactive antibodies. In this study, we investigated two laboratory developed serological assays, an enzyme linked immunosorbent assay (ELISA) and an immunofluorescent assay (IFA), developed using recombinant SARS-CoV-2 spike protein, for use in South African populations. The tests were compared with commercially available and South Africa Health Products Regulatory Authority (SAPHRA) approved assays. A panel of 100 residual diagnostic serum samples, collected prior to the pandemic, were tested on three separate occasions to determine a suitable cut-off value for differentiation of positive from negative samples. Specificity of 96 % and 100 % for ELISA and IFA respectively was demonstrated. A total of 82/89 serum samples collected between days 2-94 after onset of illness from patients with a positive molecular result were positive for IgG antibody. The sensitivity of the laboratory developed assays on samples collected > one week after onset of illness was shown to be 100 % and 98.8 % for ELISA and IFA respectively. Positive predictive values were 92.1 % for ELISA and 91.0 % for IFA using characterization of samples as positive based on confirmation of infection using RT-PCR. Serum samples (n = 62) collected from RT-PCR positive patients infected with either ancestral, or emerging variants such as Beta or Delta, tested positive for IgG antibody (62/62) using the laboratory developed assays confirming application of the assays regardless of currently circulating variant during the time of evaluation. High concordance was demonstrated between the laboratory developed assays and the commercial immunoassay among samples collected from South African populations, although the small sample size, especially for the comparison with commercial assays, must be noted. If all quality assurance controls are in place, the use of local laboratory developed assays for high-throughput screening in resource-constrained environments is a realistic alternative option.
Assuntos
COVID-19 , SARS-CoV-2 , Anticorpos Antivirais , COVID-19/diagnóstico , Ensaio de Imunoadsorção Enzimática/métodos , Humanos , Imunoglobulina G , Sensibilidade e Especificidade , África do Sul , Glicoproteína da Espícula de CoronavírusRESUMO
In March 2020, the first cases of COVID-19 were reported in South Africa. The epidemic spread very fast despite an early and extreme lockdown and infected over 600,000 people, by far the highest number of infections in an African country. To rapidly understand the spread of SARS-CoV-2 in South Africa, we formed the Network for Genomics Surveillance in South Africa (NGS-SA). Here, we analyze 1,365 high quality whole genomes and identify 16 new lineages of SARS-CoV-2. Most of these unique lineages have mutations that are found hardly anywhere else in the world. We also show that three lineages spread widely in South Africa and contributed to [~]42% of all of the infections in the country. This included the first identified C lineage of SARS-CoV-2, C.1, which has 16 mutations as compared with the original Wuhan sequence. C.1 was the most geographically widespread lineage in South Africa, causing infections in multiple provinces and in all of the eleven districts in KwaZulu-Natal (KZN), the most sampled province. Interestingly, the first South-African specific lineage, B.1.106, which was identified in April 2020, became extinct after nosocomial outbreaks were controlled. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify and control the spread of SARS-CoV-2.
RESUMO
Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.
RESUMO
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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.