Dominance of the Sars-Cov-2 501y.v2 Lineage in Gauteng - South Africa

[Mary Wilson]

National Institute For Communicable Diseases
28 JANUARY 2021

Summary

The 501Y.V2 lineage has been recently been shown to predominate in the Eastern Cape, Western Cape and KwaZulu-Natal provinces of South Africa, all of which experienced major outbreaks of COVID-19. This variant of concern harbours mutations associated with increased transmissibility and neutralizing antibody resistance. Here we describe a preliminary analysis of 479 sequences from Gauteng, the country’s economic hub, indicating that the 501Y.V2 lineage rst appeared in November and by December accounted for 84% (62/74) of sequences. The Eastern Cape, Western Cape, KwaZulu-Natal and Gauteng data suggests that 501Y.V2 lineage may be predominant throughout South Africa.

Background

Coronavirus disease 2019 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease was rst identi ed in Wuhan, China in December 2019 and has subsequently caused a global pandemic with over 99.8 million cases and 2.4 million deaths reported as of 26 January 20211. In South Africa, the rst case was reported on 5 March 2020 and as of 26 January 2021, 1.42 million cases and 41,117 deaths have been documented2.

Whole genome sequencing (WGS) has been extensively employed in response to this pandemic. As of 26 January 2021, 337,106 genome sequences from around the world were available in the GISAID public database3. Genomic data has been shown to complement epidemiological ndings and has demonstrated the ongoing evolution of the virus, which has contributed to guiding public health and infection control strategies related to SARS- CoV-24-8 [2-6].

Coronaviruses have the largest genomes of all RNA viruses with the SARS-CoV-2 genome consisting of ~30, 000 nucleotides, containing 13-15 open reading frames and encoding 12 proteins9. The virus contains 4 structural proteins, namely the spike (S), envelope (E), membrane (M) and nucleocapsid (N)9. The spike protein mediates host cell entry through receptor engagement and membrane fusion and is also the target for neutralizing antibodies9.

Since its emergence, SARS-CoV-2 has diversi ed into several different clades and lineages based on speci c mutational signatures. This includes the Nextstrain10 and Pangolin11 nomenclatures. The Nextstrain nomenclatures provide a more general overview of the diversity of SARS-CoV-2 strains circulating globally, while the Pangolin nomenclature re ects a relatively higher resolution.
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https://www.nicd.ac.za/wp-content/up...h-Africa-1.pdf

 

[Mary Wilson]

ACCEPTED MANUSCRIPT

Severe reinfection with South African SARS-CoV-2 variant 501Y.V2: A case report

Published: 10 February 2021
https://doi.org/10.1093/cid/ciab129

No?mie Zucman, Fabrice Uhel, Diane Descamps, Damien Roux, Jean-Damien Ricard

- This content is only available as a PDF. -

... We here report a case of severe SARS-CoV-2 reinfection with South African variant 501Y.V2, four months after recovering from a first episode of COVID-19. In September 2020, a 58-year old immunocompetent male with a history of asthma presented with mild fever and dyspnea. SARS- CoV-2 infection was diagnosed by real-time RT-PCR on a nasopharyngeal swab. Symptoms resolved within a few days and the patient tested negative twice in December 2020. In January 2021, 129 days after onset of the first infection, he presented to hospital for recurrent dyspnea and fever. SARS-CoV-2 RT-PCR was positive again, and viral genome sequencing identified D80A, E484K and N501Y mutations in the spike region, characterizing the 501Y.V2 lineage B.1.351 variant. Seven days later, the patient developed a severe acute respiratory distress syndrome requiring intubation and mechanical ventilation. He was treated with dexamethasone and tocilizumab. Antibody testing was positive for IgG against SARS-CoV-2. The patient was negative for HIV, and showed no biological evidence for immunological disorder. He is still in critical condition at the time of submission. The strain responsible for the first episode of COVID-19 was not available for sequencing.
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