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).
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.
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,
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.
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.
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.