The molecular evolution of SARS-CoV-2

Abstract

The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed unprecedented challenges to global public health, economies, and societies. This thesis aims to understand the transmission dynamics, evolution, and antiviral resistance of SARS-CoV-2 through next-generation sequencing.

In Chapter 3, viral genomic studies were used to investigate 3 outbreaks in Hong Kong. Using whole genome sequencing and phylogenetic analysis, the sources of the outbreak were identified, including 1) an imported case from Nepal that caused wave 4 in November 2020; 2) imported cases from travelers returning to Hong Kong that caused a housing estate outbreak due to Omicron variant in January 2022; and 3) imported hamsters from the Netherlands that cause an outbreak f Delta variant AY.127. These findings revealed the rapid spread of B.1.36.27 and Omicron variants in Hong Kong, the effectiveness of timely nonpharmaceutical interventions (NPIs) in curbing transmission, and the limitation of stringent public health measures. This Chapter also explored the transmission of SARS-CoV-2 from pet hamsters to humans, providing evidence of zoonotic transfer, and its implications for public health.

In Chapter 4, the emergence of amino acid substitutions during acute or chronic SARS-CoV-2 infection was accessed. In Chapter 4.1, in a patient with acute SARS-CoV-2 infection, the emergence of amino acid substitution in a neutralizing epitope at the N-terminal of Spike protein was found. In Chapter 4.2, de novo amino acid substitutions (DNS) in 34 chronically infected patients was identified, including 4 patients from our hospital. Many DNS that appeared in multiple patients were lineage-defining mutations of epidemiologically important SARS-CoV-2 variants, such as the Omicron variant. Most importantly, among the 4 chronically infected patients in our hospital, nsp9 T35I was found to have emerged in 3 of them. The mutation may affect the functional interaction with nsp12 in the replication and transcription complex.

In Chapter 5, the prevalence of antiviral resistance was evaluated using sequence data deposited in a public database (GISAID) up to December 2022, 1 year after the approval of Paxlovid, a 3CL protease inhibitor. We found that 0.5% (67,095/13,446,588) of the SARS-CoV-2 sequences contain nsp5 substitutions that were known to confer resistance against the 3CL protease (nsp5) inhibitors. Further analysis did not identify any particular nsp5 substitutions that are increasing in prevalence globally.

In conclusion, this thesis contributes to the understanding of the molecular evolution of SARS-CoV-2 by applying genomics sequencing to the epidemiological investigation of outbreaks, offering valuable insights into its transmission dynamics, the impact of control measures, intrahost variation, and the challenges posed by zoonotic transfer. The findings also emphasized the critical role of genomic surveillance in detecting antiviral drug resistance in a population.