Integrated Molecular and Serological Epizootic Monitoring of SARS-CoV-2 and Influenza A Virus in Animals in Kazakhstan

Respiratory viruses with broad host ranges are relevant to veterinary epidemiology, biological safety, and One Health surveillance. This retrospective study integrated companion-animal and wildlife records to examine two complementary surveillance questions: SARS-CoV-2 detection in dogs and cats with close human contact, and influenza A virus detection across a broader multispecies panel that included wild birds. We analyzed 256 archived animal samples collected in Kazakhstan during 2022–2023, comprising 158 dogs, 76 cats, and 22 animals of other domestic and wild species. A previously developed in-house multiplex RT-qPCR assay was used to detect SARS-CoV-2 and influenza A virus RNA, and a previously developed in-house SM-antigen-based ELISA was used to assess SARS-CoV-2-associated serum reactivity. SARS-CoV-2 RNA was detected in 104/256 samples (40.6%; 95% CI, 34.8–46.7), including 68 dogs and 36 cats. Influenza A virus RNA was detected in four wild birds (1.6%): two partridges and two mallards. According to the assay-specific classification recorded in the source dataset, 34 sera were reactive, 14 were doubtful, and 208 were non-reactive. All SARS-CoV-2 RT-qPCR-positive samples were ELISA-non-reactive; all reactive or doubtful ELISA results occurred among RT-qPCR-negative animals. Dogs and cats did not differ significantly in SARS-CoV-2 RT-qPCR positivity, ELISA reactivity, or Ct distributions. Because the ELISA had not been formally validated for the animal species studied, reactivity was not interpreted as confirmed SARS-CoV-2 seropositivity. The archived 2022–2023 dataset therefore provides a historical baseline for multispecies respiratory-virus surveillance in Kazakhstan and supports cautious integration of molecular and serological data.