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Article
SARS-CoV-2 Africa dashboard for real-time COVID-19 information
The SARS-CoV-2 Africa dashboard is an interactive tool that enables visualization of SARS-CoV-2 genomic information in African countries. The customizable app allows users to visualize the number of sequences ...
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Open AccessGlobal disparities in SARS-CoV-2 genomic surveillance
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic ...
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Open AccessAuthor Correction: Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection
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Open AccessEmergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19)...
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Open AccessGenomic epidemiology of the SARS-CoV-2 epidemic in Brazil
The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps r...
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Open AccessOmicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection
SARS-CoV-2 Omicron (B.1.1.529) BA.4 and BA.5 sub-lineages, first detected in South Africa, have changes relative to Omicron BA.1 including substitutions in the spike receptor binding domain. Here we isolated l...
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Open AccessOmicron infection enhances Delta antibody immunity in vaccinated persons
The extent to which Omicron infection1–9, with or without previous vaccination, elicits protection against the previously dominant Delta (B.1.617.2) variant is unclear. Here we measured the neutralization capacit...
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Open AccessComparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq
Over 4 million SARS-CoV-2 genomes have been sequenced globally in the past 2 years. This has been crucial in elucidating transmission chains within communities, the development of new diagnostic methods, vacci...
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Article
Open AccessEmergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage
Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased transmissibility, neutralization resistance and disease severity. Here we report the emergence of the PANGO lineage C...
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Open AccessAuthor Correction: T cell responses to SARS-CoV-2 spike cross-recognize Omicron
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Open AccessRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (...
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Article
Open AccessT cell responses to SARS-CoV-2 spike cross-recognize Omicron
The SARS-CoV-2 Omicron variant (B.1.1.529) has multiple spike protein mutations1,2 that contribute to viral escape from antibody neutralization3–6 and reduce vaccine protection from infection7,8. The extent to wh...
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Open AccessOmicron extensively but incompletely escapes Pfizer BNT162b2 neutralization
The emergence of the SARS-CoV-2 variant of concern Omicron (Pango lineage B.1.1.529), first identified in Botswana and South Africa, may compromise vaccine effectiveness and lead to re-infections1. Here we invest...
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Open AccessImplementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing
The rapid identification and isolation of infected individuals remains a key strategy for controlling the spread of SARS-CoV-2. Frequent testing of populations to detect infection early in asymptomatic or pres...
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Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
SARS-CoV-2 variants of concern (VOC) have arisen independently at multiple locations1,2 and may reduce the efficacy of current vaccines that target the spike glycoprotein of SARS-CoV-23. Here, using a live-virus ...
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Detection of a SARS-CoV-2 variant of concern in South Africa
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (des...
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Article
Sixteen novel lineages of SARS-CoV-2 in South Africa
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. ...
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Open AccessUnlocking the efficiency of genomics laboratories with robotic liquid-handling
In research and clinical genomics laboratories today, sample preparation is the bottleneck of experiments, particularly when it comes to high-throughput next generation sequencing (NGS). More genomics laborato...
