Influenza circulation was significantly affected in 2020–21 by the COVID-19 pandemic. During this time, few influenza cases were recorded. However, in the summer of 2021–22, an increase in atypical influenza cases was observed, leading to the resurgence of influenza in the southernmost state of Brazil, Rio Grande do Sul (RS). The present study aimed to identify FLUAV, FLUBV, and SARS-CoV-2 circulation and characterize influenza genomes in suspected COVID-19 patients using high-throughput sequencing technology. Respiratory samples (n = 694) from patients in RS were selected between July 2021 and August 2022. The samples were typed reverse transcriptase real-time PCR (RT-qPCR) and showed 32.13% (223/694) of the samples to be positive for SARS-CoV-2, 7.06% for FLUAV (49/694). FLUBV was not detected. RT-qPCR data also showed 0.57% of the cases had FLUAV and SARS-CoV-2 co-infections. Whole genome sequencing of the FLUAV positive specimens produced 15 complete genomes of H3N2 subtype with phylogenetic placement in the 3C.2a1b.2a.2a.3 subclade. Mutation analysis showed 73 amino acid substitutions in addition to several nonsynonymous mutations. The detected percentage of FLUAV (7.06%) is relatively similar to the total number of flu cases requiring hospitalization in RS state (8.9%), including those admitted to intensive care units for severe complications. This study provides insights into influenza virus circulation in the south of Brazil during the Omicron wave of the COVID-19 pandemic and reinforces the importance of H3N2 as a major driver of severe respiratory disease in the region along with the SARS-CoV-2 Omicron wave at the beginning of 2022.

Animals are common hosts for many coronaviruses where bats and rodents are commonly regarded as primary reservoirs. The unquestionable emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a yet unknown animal host - in addition with reports of further anthropogenic spread and sustained transmission in mustelids, captive felids, and domestic dogs and cats owned by people previously tested as SARS-CoV-2-positive, rise some concerns about possible continuous maintenance of the virus in nature and domestic species. In this review, we discussed the current data about coronaviruses in domestic and farming animals, recombination events, animal species susceptibility, virus-cell receptor interactions, and clinical signs of most relevant Coronaviridae members of each genera. Also, we present what is known about SARS-CoV-2 in animals and what will be the potential role of those species in COVID-19 epidemiology. Apparently, the virus can infect pets on some occasions, where cats look to be more susceptible than dogs. Thus, pet infection by sick owners is not only likely but expected given the numerous opportunities for spill-over during a massive outbreak. Regarded to farm animals, attention should be focused on breeding species of the Mustelidae family since they are those that have been shown to be more susceptible in experimental infections and have also effectively exhibited animal-to-human transmission. Other intensively bred species such as poultry, swine, horses and ruminants seem to present little or no epidemiological risk so far. The continuous monitoring of SARS-CoV-2 in animals in close contact with people with COVID-19 may be a key in the understanding of this emergent disease and the animal’s role in epidemiology in the future. It is possible that some species will serve as important reservoirs and source of infection of COVID-19 for humans making it re-emergent in the future, as is theoretically proposed for the origin of SARS-CoV-2.