SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022

Abstract

Intra-host diversity studies are used to characterise the mutational heterogeneity of SARS-CoV-2 infections in order to understand the impact of virus-host adaptations. This study investigated the frequency and diversity of the spike (S) protein mutations within SARS-CoV-2 infected South African individuals. The study included SARS-CoV-2 respiratory samples, from individuals of all ages, received at the National Health Laboratory Service at Charlotte Maxeke Johannesburg Academic hospital, Gauteng, South Africa, from June 2020 to May 2022. Single nucleotide polymorphism (SNP) assays and whole genome sequencing were performed on a random selection of SARS-CoV-2 positive samples. The allele frequency (AF) was determined using TaqMan Genotyper software for SNP PCR analysis and galaxy.eu for analysis of FASTQ reads from sequencing. The SNP assays identified 5.3% (50/948) of Delta cases with heterogeneity at delY144 (4%; 2/50), E484Q (6%; 3/50), N501Y (2%; 1/50) and P681H (88%; 44/50), however only heterogeneity for E484Q and delY144 were confirmed by sequencing. From sequencing we identified 9% (210/2381) of cases with Beta, Delta, Omicron BA.1, BA.2.15, and BA.4 lineages that had heterogeneity in the S protein. Heterogeneity was primarily identified at positions 19 (1.4%) with T19IR (AF 0.2–0.7), 371 (92.3%) with S371FP (AF 0.1–1.0), and 484 (1.9%) with E484AK (0.2–0.7), E484AQ (AF 0.4–0.5) and E484KQ (AF 0.1–0.4). Mutations at heterozygous amino acid positions 19, 371 and 484 are known antibody escape mutations, however the impact of the combination of multiple substitutions identified at the same position is unknown. Therefore, we hypothesise that intra-host SARS-CoV-2 quasispecies with heterogeneity in the S protein facilitate competitive advantage of variants that can completely/partially evade host’s natural and vaccine-induced immune responses.

VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance

“…A novel SARS-CoV-2 variant B.1.1.529 was identified in Southern Africa and flagged as containing a potentially concerning number of spike mutations on 23rd November 2021 following sequence identification in Botswana (3 genomes), and Hong Kong ex S. Africa (1 genome, partial) 20 . South African public health recorded an extremely large and rapid increase in SARS-CoV-2 cases and test positivity in Gauteng Province for the week of 14–20 November 2021 21 with this rapidly attributed to Omicron by South Africa Centre for Epidemic Response and Innovation 22 , 23 . It was designated by WHO and named Omicron VOC on 26th November 2021.…”

“…A novel SARS-CoV-2 variant B.1.1.529 was identified in Southern Africa and flagged as containing a potentially concerning number of spike mutations on 23rd November 2021 following sequence identification in Botswana (3 genomes), and Hong Kong ex S. Africa (1 genome, partial) 20 . South African public health recorded an extremely large and rapid increase in SARS-CoV-2 cases and test positivity in Gauteng Province for the week of 14-20 November 2021 21 with this rapidly attributed to Omicron by South Africa Centre for Epidemic Response and Innovation 22,23 www.nature.com/scientificreports/ coverage 24 and early laboratory studies indicated significant reduction in neutralising ability of vaccine and prior-infection induced antibodies [25][26][27] . This reinfection and incomplete vaccine protection risk has been borne out in populations of higher vaccination coverage following Omicron introduction in the U.K. with the variant rapidly becoming dominant against a background of high Delta caseload.…”