Household clusters of SARS-CoV-2 Omicron subvariants contemporaneously sequenced from dogs and their owners

Monitoring the zoonotic potential of emerging SARS-CoV-2 variants in animals is a critical tool to protect public health. We conducted a longitudinal study in 47 households reporting people with COVID-19 in Texas in January-July 2022, during the first Omicron wave. We evaluated 105 people and 100 of their companion animals by RT-qPCR for SARS-CoV-2 at three sequential sampling events 1-2 weeks apart, starting 0-5 days after the first reported diagnosis of COVID-19 in the house. Of 47 households that reported people with COVID-19, SARS-CoV-2 was detected in 43, with 68% of people testing positive by RT-qPCR; 95.5% of people had antibodies to SARS-CoV-2. Dogs were the only animal species positive by RT-qPCR (5.4%; 3/55). Viral copies were consistently lower in dogs than household members, and no infectious virus was recovered in cell culture. Whole genome sequencing revealed household clusters of Omicron subvariants BA.1.1, BA.2.3.4 and BA.5.1.1 in people, dogs and a food bowl, confirming human-to-dog transmission within households, with no evidence of onward transmission from the infected dogs. Eleven dogs (n = 55) and two cats (n = 26) had neutralizing antibodies against SARS-CoV-2. Infection was not associated with clinical signs in pets; only two animals that tested negative for SARS-CoV-2 were reported to be sick. Nearly one-third (30.2%) of households with active COVID-19 had pets exposed to SARS-CoV-2, similar to our pre-Omicron studies, yet incidence of infection in cats was lower compared to pre-Omicron. These differences suggest that the zoonotic transmission dynamics in households may differ based on variant.