Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck

Abstract

The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.

Fig 1. Experimental timeline.

Schematic representing the sampling timeline for the three transmission pairs. Index cats were inoculated on day 0 with 5.2e5 PFU of a human isolate (hCoV-19/Japan/UT-NCGM02/2020) and were co-housed with a naive cat starting on day 1. Within each transmission pair, the top row of circles represents the index cat and the bottom row represents the contact cat. Open circles represent days on which there was no detectable infectious virus as indicated by plaque assay, and closed circles highlight days when live virus was recovered. Circles with a red outline indicate timepoints which were used in the beta-binomial estimate to calculate transmission bottleneck sizes.

Fig 2. Within-host diversity of SARS-CoV-2 viruses in domestic cats.

A) Plot representing all variants (iSNVs and indels) detected in any cat at any timepoint. Variant frequencies are plotted by genome location and are colored by gene. Circles represent synonymous iSNVs, squares represent nonsynonymous iSNVs, and stars represent indels. B) iSNV frequency spectrums with error bars showing standard deviation for index cats plotted against a “neutral model” (light gray bars) which assumes a constant population size and the absence of selection.

Fig 3. Frequency of iSNVs over time in each index and contact cat.

The frequency of iSNVs discussed in the results over time in all six cats are shown. All iSNVs over time are shown in S2 Fig and all indels over time are shown in S3 Fig. Each variant is colored by gene location. Nonsynonymous variants are plotted with solid lines and synonymous variants are plotted with dashed lines. Variants detected in index cats are denoted with squares and variants detected in contact cats are denoted with circles. Timepoints with viral loads too low to yield high quality sequences are shown by the gaps in data, but iSNVs are connected across these gaps using light lines for readability (i.e. cat 1 day 9). The dotted line at 50% frequency represents the consensus threshold.

Fig 4. SARS-CoV-2 transmission is defined by a narrow bottleneck.

Variant frequencies in the index cats (x-axis) compared with frequencies of the same variants in the corresponding contact cats (y-axis) that were used in the beta-binomial estimate are shown on the left. Estimates of SARS-CoV-2 transmission bottleneck with 99% confidence intervals shown on the right.