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Fast-spreading COVID variant can elude immune responses

Evidence that a variant of the coronavirus identified in South Africa might compromise immunity sparks concerns about vaccine effectiveness.

Alarming COVID variants show vital role of genomic surveillance

Efforts to track SARS-CoV-2 sequences have helped identify worrying variants — but researchers are blind to emerging mutations in some regions.

Genome Detective Coronavirus variant typing tool

Phylogenetic identification of variants 501Y.V1, 501Y.V2, 501Y.V3 (B.1.1.7, B.1.351, P.1 / Nextstrain 20I, 20H, 20J). Tool also determines nucleotide (NT), amino acids (AA) and codon (CDS) mutations. The mutations list are provided in html and excel formats.

Answers to 9 crucial questions about the coronavirus variants spreading around the world

Experts worldwide are urgently studying three coronavirus variants to understand what risks they pose. One variant first identified in the UK, one in South Africa, and one in Japan are probably more contagious than the original strain. They have caused cases to surge and the three nations to lock down. Here are nine key questions about the variants, answered.

Will vaccines work against the new COVID variants? Scientists race to find out

One year later and the new coronavirus is still posing new questions for researchers. The recent emergence of new COVID-19 variants across the world has left scientists searching for answers once again as they try to understand what these changes mean for the pandemic — and vaccine roll-outs. As South Africa awaits the arrival of its first shipment of COVID vaccines there are growing concerns about a new coronavirus variant — known as 501Y.V2 — circulating in the country, and what the changes in the virus could mean for how well the jabs work.

As Coronavirus Mutates, the World Stumbles Again to Respond

A South African tip led to the discovery of mutations around the world. With infections skyrocketing, 'it’s a race against time.'. Doctors and nurses at a South African hospital group noticed an odd spike in the number of Covid-19 patients in their wards in late October...

‘A bloody mess’: Confusion reigns over naming of new COVID variants

As more lineages emerge, researchers are struggling with a patchwork of nomenclature.

KRISP SCIENTIFIC PUBLICATIONS

Escape of SARS-CoV-2 501Y.V2 variants from neutralization by convalescent plasma.
Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Balazs AB, Gosnell BI, Hanekom W, Moosa MYS, NGS-SA, COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A, medRxiv (2021), 250224v1-Sigal:.

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa.
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenço J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.12.21.20248640:.

Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase.
Siedner MJ, Moorhouse MA, Simmons B, de Oliveira T, Lessells R, Giandhari J, Kemp SA, Chimukangara B, Akpomiemie G, Serenata Cm, Venter WDF, HillA, Gupta RK, Nature Communications (2020), https://doi.org/10.1038/s41467-020-19801-x:.

HIV infection alters SARS-CoV-2 responsive immune parameters but not clinical outcomes in COVID-19 disease.
Karim F, Gazy I, Cele S, Zungu Y, Krause R, Bernstein M, Ganga Y, Rodel H, Mthabela N, Mazibuko M, Khan K, Muema D, Ramjit D, Lustig G, Ndung’u T, Hanekom W, Gosnell BI, COMMIT-KZN Team, Wong E, de Oliveira T, Moosa MYS, Leslie A, Kløverpris H, Sigal A, medRxiv (2020), doi: https://doi.org/10.1101/2020.11.23.20236828:.

High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity.
San EJ, Ngcapu S, Kanzi A, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Khanyile KS, Lessells R, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.11.15.20231993:.

Cost-effectiveness of public health strategies for COVID-19 epidemic control in South Africa: a microsimulation modelling study.
Reddy KP, Shebl FM, Foote JHA, Harling G, Scott JA, Panella C, Fitzmaurice KP, Flanagan C, Hyle EP, Neilan AM, Mohareb AM, Bekker L-G, Lessells R, Ciaranello AL, Wood R, Losina E, Freedberg KA, Kazemian P, Siedner MJ , Lancet Global Health (2020), https://doi.org/10.1016/S2214-109X(20)30452-6:.

Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown.
Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Allam M, Ismail A, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Pettruccione F, Sigal A, Gazy I, Hardie D, Hsiao M, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenco J, Alcantara LCJ, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.10.28.20221143:.

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New concerns raised over South African variant of COVID-19
By: CBS News

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