Sars-Cov-2 Sequencing Update 08 July2024

SARS-CoV-2 Sequencing Update 08 July 2024 Network for Genomic Surveillance in South Africa (NGS-SA) Prepared by the National Institute for Communicable Diseases (NICD) of the National Health Laboratory (NHLS) on behalf of the Network for Genomics Surveillance in South Africa (NGS-SA)The genomic data presented here are based on South African SARS-CoV-2 sequence data downloaded from GISAID (www. [...] (2017) Data, disease and diplomacy: GISAID’s innovative contribution to global health. [...] (2017) GISAID: Global initiative on sharing all influenza data – from vision to reality. EuroSurveillance, 22(13) DOI: 10.2807/1560-7917. [...] BA.2.86 lineages (parent lineage of JN.1) continue to be detected but have declined in prevalence. [...] • Although based on small numbers, JN.1.11.1* lineages were dominant (43%) in June. [...] • Recombinant XDD.1.1 (EG.5.1.1 and JN.1.1) has been detected in Gauteng (n=6) and the Western Cape (n=22). [...] • JN.1.11.1.* lineages, specifically the variants under monitoring (VUM) KP.2 (n=16) and KP.3 (n=3), have been detected in Gauteng, Limpopo and the Western Cape between February and June. [...] Spike protein mutation* profile of Variants of Interest and Concern *Only mutations present in Omicron, Delta, or recombinant sequences are pictured • Multiple changes within the two immunogenic regions in S1 (NTD and RBD) • Including a three amino acid insertion • Accumulation of mutations surrounding the furin cleavage site • Including combination of N679K and P681H • Effect of most spike S2 su [...] Number of selected samples will depend on the size of laboratory and how many other laboratories are drained by the submitting laboratory. [...] Ct values less than 30 for more than 1 month post-primary diagnosis) in immunocompromised individuals • Possible animal-to-human transmission • Suspected cases of importation from another country, especially countries known to harbour SARS-CoV-2 variants of concern or countries with little available information • Clusters of “unusual” cases (e.g., in terms of disease presentation, patient groups