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

Braun, Katarina M.; Moreno, Gage K.; Halfmann, Peter; Hodcroft, Emma B.; Baker, David; Boehm, Emma; Weiler, Andrea M.; Haj, Amelia K.; Hatta, Masato; Maemura, Tadashi; Kawaoka, Yoshihiro; Koelle, Katia; O’Connor, David H.; Friedrich, Thomas C.

doi:10.1101/2020.11.16.384917

Cited by 26 publications

(29 citation statements)

References 70 publications

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“…The estimated bottleneck sizes were 6 (P03 and P11) and 8 (P23 and P24) for the two intra-household pairs ( Supplementary Table 5 ). The observed narrow bottleneck is consistent with two recent studies of SARS-CoV-2 ( 13 , 14 ). Nonetheless, a loose transmission bottleneck was also observed ( 8 ).…”

Section: Resultssupporting

confidence: 92%

Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

Wang

Sun

et al. 2021

Front. Med.

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The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions.

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Section: Resultssupporting

confidence: 92%

Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

Wang

Sun

et al. 2021

Front. Med.

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“…Lythgoe et al in particular used extensive controls and validation for preventing contamination and identifying sequencing errors. Other studies both in humans and in domestic cats have estimated small bottlenecks 36 , 37 . It is difficult to interpret these contrasting results because each study used different sequencing and analysis methodologies.…”

Section: Discussionmentioning

confidence: 99%

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

Valesano

Rumfelt

Dimcheff

et al. 2021

Preprint

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Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.

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“…Spike amino acid 655 is located near the S1/S2 cleavage site of the spike protein between the RBD and the fusion peptide. This variant has been reported to be under positive selection in experimentally inoculated cats ( 35 ) and has been shown to emerge following one passage of pseudotyped SARS-CoV-2 in cell culture in the presence of anti-spike human antibodies ( 36 ).…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection

Bashor

Gagne

Bosco‐Lauth

et al. 2021

Preprint

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SARS-CoV-2 spillback from humans into domestic and wild animals has been well-documented. We compared variants of cell culture-expanded SARS-CoV-2 inoculum and virus recovered from four species following experimental exposure. Five nonsynonymous changes in nsp12, S, N and M genes were near fixation in the inoculum, but reverted to wild-type sequences in RNA recovered from dogs, cats and hamsters within 1-3 days post-exposure. Fourteen emergent variants were detected in viruses recovered from animals, including substitutions at spike positions H69, N501, and D614, which also vary in human lineages of concern. The rapidity of in vitro and in vivo SARS-CoV-2 selection reveals residues with functional significance during host-switching, illustrating the potential for spillback reservoir hosts to accelerate evolution, and demonstrating plasticity of viral adaptation in animal models.

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

Cited by 26 publications

References 70 publications

Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection

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