Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern
Authors: Tapfumanei Mashe, Faustinos Tatenda Takawira, Hlanai Gumbo, Agnes Juru, Charles Nyagupe, Kenneth K Maeka, Sekesai Mtapuri-Zinyowera, Muchaneta Gudza-Mugabe, Leonardo de Oliveira Martins, Justin O'Grady, Robert A Kingsley, Andrew J Page, Raiva Simbi
Journal: The Lancet Microbe (2021)

Less than 5% (23 815 of 537 360) of public SARS-CoV-2 genomes are from low-income and middle-income countries, where 80% of the world's population resides and has been similarly affected by COVID-19. The recent, worldwide spread of variants of concern has highlighted the need for global vigilance. Prospective surveillance of SARS-CoV-2 by genome sequencing in Zimbabwe between December, 2020, and January, 2021 (the period of the so-called second wave), has identified that variants with concerning mutations are prevalent in sequenced samples. In December, 2020, 95 (89%) of 107 sequenced cases contained mutations of concern, rising to 102 (98%) of 104 in January, 2021. The identified variants included the previously reported B.1.351 (501Y.V2) and A.23.1 variants, along with a novel variant under investigation (C.2).1Bugembe DL Phan MVT Ssewanyana I et al.A SARS-CoV-2 lineage A variant (A.23·1) with altered spike has emerged and is dominating the current Uganda epidemic.medRxiv. 2021; (published online Feb 11.) (preprint).https://doi.org/10.1101/2021.02.08.21251393Google Scholar, 2Tegally H Wilkinson E Giovanetti M et al.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.medRxiv. 2020; (published online Dec 22.) (preprint).https://doi.org/10.1101/2020.12.21.20248640Google Scholar, 3Welkers MRA Han AX Reusken CBEM Eggink D Possible host-adaptation of SARS-CoV-2 due to improved ACE2 receptor binding in mink.Virus Evol. 2021; 7veaa094Crossref PubMed Scopus (39) Google Scholar The B.1.1.7, B.1.525, P.1, and P.2 and variants were not identified in Zimbabwe. Variants with concerning mutations have all replaced previously identified lineages in Zimbabwe (appendix).4Mashe T Takawira FT de Oliveira Martins L et al.Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread.medRxiv. 2021; (published online Jan 6.) (preprint).https://doi.org/10.1101/2021.01.04.20232520Google Scholar Firstly, the B.1.351 variant of concern, originally identified in South Africa,2Tegally H Wilkinson E Giovanetti M et al.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.medRxiv. 2020; (published online Dec 22.) (preprint).https://doi.org/10.1101/2020.12.21.20248640Google Scholar accounted for 74 (69%) of 107 sequenced cases in December, 2020, and 99 (95%) of 104 sequenced cases in January, 2021. The population structure was consistent with multiple separate introductions. Zimbabwe is the second country other than South Africa to report B.1.351 as the dominant variant to date.5Mwenda M Saasa N Sinyange N et al.Detection of B. 1·351 SARS-CoV-2 variant strain—Zambia, December 2020. MMWR.Morb Mortal Wkly Rep. 2021; 70: 280-282Crossref PubMed Scopus (87) Google Scholar As in other countries, this variant has been associated with increased transmissibility, resulting in overwhelmed health-care systems and in higher mortality than the first wave (appendix). Secondly, the A.23.1 variant of concern, first reported in Uganda,1Bugembe DL Phan MVT Ssewanyana I et al.A SARS-CoV-2 lineage A variant (A.23·1) with altered spike has emerged and is dominating the current Uganda epidemic.medRxiv. 2021; (published online Feb 11.) (preprint).https://doi.org/10.1101/2021.02.08.21251393Google Scholar was observed in 3 (3%) of 107 sequenced cases in December, but was not observed in 104 sequenced cases in January. Thirdly, a variant designated C.2 and containing a spike protein mutation (N501T) that was previously reported in another lineage of SARS-CoV-2 found in mink was present in Zimbabwe in both December, 2020, and January, 2021. N501T is thought to improve ACE2 receptor binding in mink.3Welkers MRA Han AX Reusken CBEM Eggink D Possible host-adaptation of SARS-CoV-2 due to improved ACE2 receptor binding in mink.Virus Evol. 2021; 7veaa094Crossref PubMed Scopus (39) Google Scholar A mutation in the same location, N501Y, is associated with increased transmissibility in humans. In December, 2020, 18 (15%) of 117 of cases were found to be of the C.2 variant, whereas in January, 2021, this number fell to 3 (3%) of 104. Phylogenetic analysis of international genomes of the C.2 variant indicated that they were interspersed with C.2 genomes from Zimbabwean cases, indicating that Zimbabwe was a possible source. In conclusion, variants with concerning mutations identified in December, 2020, and January, 2021, have replaced previously identified lineages in Zimbabwe.4Mashe T Takawira FT de Oliveira Martins L et al.Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread.medRxiv. 2021; (published online Jan 6.) (preprint).https://doi.org/10.1101/2021.01.04.20232520Google Scholar This observation highlights the importance of global surveillance by whole-genome sequencing of SARS-CoV-2 to identify sources and transmission routes, and to provide supporting evidence for policy decisions. This research was partly funded by the Biotechnology and Biological Sciences Research Council Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352. We declare no competing interests. This Correspondence is dedicated to the memory of Sekesai Mtapuri-Zinyowera, who died on March 4, 2021. 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