Richard Lessells
A5062343676- SARS-CoV-2 and COVID-19 Research
- HIV/AIDS Research and Interventions
- HIV Research and Treatment
- HIV/AIDS drug development and treatment
- Tuberculosis Research and Epidemiology
- SARS-CoV-2 detection and testing
- COVID-19 epidemiological studies
- COVID-19 Clinical Research Studies
- Viral Infections and Outbreaks Research
- vaccines and immunoinformatics approaches
- Pneumocystis jirovecii pneumonia detection and treatment
- HIV/AIDS Impact and Responses
- Animal Virus Infections Studies
- Vaccine Coverage and Hesitancy
- Bacillus and Francisella bacterial research
- Bacteriophages and microbial interactions
- HIV, Drug Use, Sexual Risk
- Viral gastroenteritis research and epidemiology
- Pneumonia and Respiratory Infections
- Hepatitis C virus research
- Hepatitis B Virus Studies
- Infectious Diseases and Tuberculosis
- Mosquito-borne diseases and control
- Adolescent Sexual and Reproductive Health
- CRISPR and Genetic Engineering
University of KwaZulu-Natal
2016-2025
Centre for the AIDS Programme of Research in South Africa
2018-2025
London School of Hygiene & Tropical Medicine
2014-2023
Stellenbosch University
2014-2023
Africa Health Research Institute
2017-2023
Response Biomedical (Canada)
2023
University of Cape Town
2023
University of London
2012-2022
University of the Witwatersrand
2018-2021
Duke Medical Center
2021
Abstract The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and,...
Summary Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts world is creating conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations spike protein, including three at important residues receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This emerged South Africa after first epidemic wave...
Abstract The emergence of the SARS-CoV-2 variant concern Omicron (Pango lineage B.1.1.529), first identified in Botswana and South Africa, may compromise vaccine effectiveness lead to re-infections 1 . Here we investigated escape from neutralization by antibodies African individuals vaccinated with Pfizer BNT162b2. We used blood samples taken soon after vaccination who were previously infected or no evidence previous infection. isolated sequence-confirmed live virus an person observed that...
Abstract Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 BA.5, responsible for a fifth wave infections. The spike proteins BA.5 are identical, similar to except addition 69–70 deletion (present in Alpha BA.1 lineage), L452R Delta variant), F486V wild-type amino acid at Q493. differ...
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 the country full lockdown (Oxford stringency index of 90)1. Despite early response, November over 785,000 people were infected, which accounted for approximately 50% all known African infections2. In this study, we analyzed 1,365 near whole genomes report identification 16 new lineages SARS-CoV-2 isolated between 6 August 2020. Most these have unique...
The emergence of SARS-CoV-2 Omicron, first identified in Botswana and South Africa, may compromise vaccine effectiveness the ability antibodies triggered by previous infection to protect against re-infection (1). Here we investigated whether Omicron escapes antibody neutralization Africans, either previously infected or uninfected, who were vaccinated with Pfizer BNT162b2. We also if requires ACE2 receptor infect cells. isolated sequence confirmed live virus from an person Africa compared...
We propose a novel, non-discriminatory classification of monkeypox virus diversity. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order detection. Within IIb, cause current global outbreak, identified multiple lineages (A.1, A.2, A.1.1 B.1) to support real-time genomic surveillance.
Background Increased mortality among men on antiretroviral therapy (ART) has been documented but remains poorly understood. We examined the magnitude of and risk factors for gender differences in ART. Methods Findings Analyses included 46,201 ART-naïve adults starting ART between January 2002 December 2009 eight programmes across South Africa (SA). Patients were followed from initiation to outcome or analysis closure. The primary was mortality; secondary outcomes loss follow-up (LTF),...
<ns3:p>Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations biological concern were reported, one the United Kingdom and South Africa. Using a combination data from routine surveillance, genomic sequencing international travel we track dispersal lineages B.1.1.7 B.1.351 (variant 501Y-V2). We account for potential biases surveillance efforts by including passenger volumes location where lineage was first London Africa...
<ns3:p>Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations biological concern were reported, one the United Kingdom and South Africa. Using a combination data from routine surveillance, genomic sequencing international travel we track dispersal lineages B.1.1.7 B.1.351 (variant 501Y-V2). We account for potential biases surveillance efforts by including passenger volumes location where lineage was first London Africa...
Characterizing SARS-CoV-2 evolution in specific geographies may help predict properties of the variants that come from these regions. We mapped neutralization a strain evolved over 6 months ancestral virus person with advanced HIV disease South Africa; this was infected prior to emergence Beta and Delta variants. longitudinally tracked tested it against self-plasma convalescent plasma ancestral, Beta, infections. Early similar but multitude mutations found Omicron other It showed substantial...
SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because patchy data. Wilkinson et al . curated viral genomes collected 2021 from several countries continent. Outbreaks during 2020 each country were initiated by imported cases, mostly Europe. As developed, case numbers likely many times higher than reported, and subsequent waves appear have more severe. Consequently,...
SARS-CoV-2 Omicron (B.1.1.529) BA.4 and BA.5 sub-lineages, first detected in South Africa, have changes relative to BA.1 including substitutions the spike receptor binding domain. Here we isolated live viruses measured BA.4/BA.5 neutralization elicited by infection either absence or presence of previous vaccination as well from without infection. In BA.1-infected unvaccinated individuals, declines 7.6-fold for 7.5-fold BA.5. vaccinated individuals with subsequent infection, decreases...
Abstract SARS-CoV-2 variants of concern (VOC) have arisen independently at multiple locations and may reduce efficacy current vaccines targeted the spike glycoprotein. We re-cently described emergence VOC in South Africa (501Y.V2 or PANGO lineage B.1.351) with mutations receptor-binding domain (RBD) N-terminal (NTD). Here, using a live virus neutralization assay (LVNA), we compared first wave (B.1.1.117) versus 501Y.V2 variant plasma collected from adults hospitalized COVID-19 two African...
The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves Western Cape, assess contribution of undiagnosed infection differences a context high seroprevalence due and determine whether protection against severe disease conferred by and/or vaccination maintained.
Among the 30 nonsynonymous nucleotide substitutions in Omicron S-gene are 13 that have only rarely been seen other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of at sites will likely impact (1) interactions between subunits Spike trimer and predisposition to shift from down up configurations, (2) with ACE2 receptors, (3) priming for membrane fusion. We show here that, based on both rarity these intrapatient sequencing reads patterns selection...
The SARS-CoV-2 Omicron (B.1.1.529) variant first emerged as the BA.1 sub-lineage, with extensive escape from neutralizing immunity elicited by previous infection other variants, vaccines, or combinations of both 1,2 . Two new sub-lineages, BA.4 and BA.5, are now emerging in South Africa changes relative to BA.1, including L452R F486V mutations spike receptor binding domain. We isolated live BA.5 viruses tested them against participants who were Omicron/BA.1 infected but unvaccinated (n=24)...
Abstract South Africa’s fourth COVID-19 wave was driven predominantly by three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant concern. We have now identified two new lineages, BA.4 BA.5. The spike proteins BA.5 are identical, comparable to except for addition 69-70del, L452R, F486V wild type amino acid at Q493. 69-70 deletion in allows these be proxy marker S-gene target failure with TaqPath™ qPCR assay. rapidly replaced BA.2, reaching more than 50% sequenced cases Africa...
We aimed to assess the effectiveness of a single dose Ad26.COV2.S vaccine (Johnson & Johnson) in health-care workers South Africa during two waves African COVID-19 epidemic.
Abstract The extent to which Omicron infection 1–9 , with or without previous vaccination, elicits protection against the previously dominant Delta (B.1.617.2) variant is unclear. Here we measured neutralization capacity variants of severe acute respiratory syndrome coronavirus 2 in 39 individuals South Africa infected sublineage BA.1 starting at a median 6 (interquartile range 3–9) days post symptom onset and continuing until last follow-up sample available, 23 19–27) symptoms allow...