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.

Figure 1.

Serial interval and timing of sample collection. (A) Days between index symptom onset and household contact symptom onset for the indicated clades. “Non-VOC” includes all lineages not designated as a WHO variant of concern. No Beta variant transmission pairs were analyzed. (B) Days between symptom onset and collection of the sequenced specimen for the index case. Index cases from MHome are indicated in teal, and index cases from HIVE are indicated in red. Omicron had a shorter time between index symptom onset and sample collection for sequencing than non-VOC (df=3, F=8.138, p <0.001) and HIVE households had a shorter time than MHome households (df =1, F =15.363, p < 0.001). (C) RT-qPCR cycle threshold values (inverted y-axis) for all specimens collected from index cases. Sequenced specimens are indicated with filled circles.

Figure 2.

Genetic diversity in sequenced specimens. (A) Histogram of the number of iSNV per specimen. (B) iSNV frequency histogram.

Figure 3.

Diversity across transmission pairs. (A) The number of individuals per household with sequenced specimens. Colors represent the different clades. (B) Shared genetic diversity between transmission pairs. Each point is an iSNV within a transmission pair. Red points indicate mutation C29708T, which was shared in a single household.