San, James E, Ngcapu, Sinaye, Kanzi, Aquillah M, Tegally, Houriiyah, Fonseca, Vagner, Giandhari, Jennifer, Wilkinson, Eduan, Nelson, Chase W, Smidt, Werner, Kiran, Anmol M 
ORCID: 0000-0003-2680-2303 et al (show 9 more authors)
(2021)
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.
VIRUS EVOLUTION, 7 (1).
veab041-.
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Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.pdf - Published version Download (1MB) | Preview |
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in humans and a wide range of animal species. Its rapid global spread has resulted in a major public health emergency, necessitating commensurately rapid research to improve control strategies. In particular, the ability to effectively retrace transmission chains in outbreaks remains a major challenge, partly due to our limited understanding of the virus' underlying evolutionary dynamics within and between hosts. We used high-throughput sequencing whole-genome data coupled with bottleneck analysis to retrace the pathways of viral transmission in two nosocomial outbreaks that were previously characterised by epidemiological and phylogenetic methods. Additionally, we assessed the mutational landscape, selection pressures, and diversity at the within-host level for both outbreaks. Our findings show evidence of within-host selection and transmission of variants between samples. Both bottleneck and diversity analyses highlight within-host and consensus-level variants shared by putative source-recipient pairs in both outbreaks, suggesting that certain within-host variants in these outbreaks may have been transmitted upon infection rather than arising <i>de novo</i> independently within multiple hosts. Overall, our findings demonstrate the utility of combining within-host diversity and bottleneck estimations for elucidating transmission events in SARS-CoV-2 outbreaks, provide insight into the maintenance of viral genetic diversity, provide a list of candidate targets of positive selection for further investigation, and demonstrate that within-host variants can be transferred between patients. Together these results will help in developing strategies to understand the nature of transmission events and curtail the spread of SARS-CoV-2.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | bottleneck, NGS whole-genome sequencing, nonsynonymous, SARS-CoV-2, selection, South Africa, transmission dynamics, within-host variants |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 23 May 2022 07:37 |
| Last Modified: | 18 Jan 2023 21:01 |
| DOI: | 10.1093/ve/veab041 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3155275 |
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