Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants

Abstract

Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of natural selection along a transmission chain. Many viruses exhibit tight bottlenecks, and studies of early SARS-CoV-2 lineages identified a bottleneck of 1-3 infectious virions. While increased force of infection, host receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here, we compare the transmission bottleneck of non-variant-of-concern (non-VOC) SARS-CoV-2 lineages to those of the Alpha, Delta, and Omicron variants. We sequenced viruses from 168 individuals in 65 multiply infected households in duplicate to high depth of coverage. In 110 specimens collected close to the time of transmission, within-host diversity was extremely low. At a 2% frequency threshold, 51% had no intrahost single nucleotide variants (iSNV), and 42% had 1-2 iSNV. In 64 possible transmission pairs with detectable iSNV, we identified a bottleneck of 1 infectious virion (95% CI 1-1) for Alpha, Delta, and Omicron lineages and 2 (95% CI 2-2) in non-VOC lineages. The latter was driven by a single iSNV shared in one non-VOC household. The tight transmission bottleneck in SARS-CoV-2 is due to low genetic diversity at the time of transmission, a relationship that may be more pronounced in rapidly transmissible variants. The tight bottlenecks identified here will limit the development of highly mutated VOC in typical transmission chains, adding to the evidence that selection over prolonged infections in immunocompromised patients may drive their evolution.

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

“…This persistent intrahost evolution may accelerate antigenic alteration and lead to the emergence of genetically distinct subvariants (Smith and Ashby, 2022;Ahmadi et al, 2023;Chaguza et al, 2023). Bendall et al (2023) observed a tight transmission bottleneck that would limit the development of highly mutated VOCs in the transmission chain of acutely infected individuals, further suggesting that selection for long-term infection in immunocompromised patients may drive SARS-CoV-2 VOC evolution (Braun et al, 2021;Wilkinson et al, 2022). Surveillance by sequencing is recommended for (i) patients carried with SARS-CoV-2, (ii) patients suspected of reinfection, and (iii) patients who are immunocompromised (Landis et al, 2023).…”

Pathways to altered virulence of SARS-CoV-2

“…The secondary spread of the virus through the host tissues, while strongly impacting virulence and intrahost evolution, is unlikely to impact viral transmission from one host to the next. As the bolus of viral particles required to seed an infection is extremely small (147,148), a narrow bottleneck exists at the point of transmission (147,149). This bottleneck, in general, serves to slow SARS-CoV-2 evolution, and may make it challenging for natural selection to act on viral traits that specifically increase intrahost spread (150).…”