Abstract
Introduction Between November 2023 and January 2024, a severe gastroenteritis outbreak with high mortality occurred among working dogs based in the Almaty region of Kazakhstan. The epidemic was characterized by an acute onset, rapid progression, and resulted in the death of over 100 juveniles (under 12-month-old) and several vaccinated adult dogs. In this study, we investigated the co-occurrence of canine circovirus and canine parvovirus DNAs in clinical samples from affected dogs, performed genetic characterization of the identified viruses, and evaluated their role in the outbreak. Methods Polymerase Chain Reaction and Massive Parallel Sequencing methods were used in this research. Results Polymerase chain reaction analysis of clinical samples revealed the presence of canine parvovirus in eight of the ten samples examined. Further, high-throughput sequencing of pooled oral, rectal, and blood swabs revealed that the majority of viral sequences corresponded to viruses in the Circovirus genus (Circoviridae, 42.3%), followed by Protoparvovirus genus (Parvoviridae, 38%), together accounting for over 80% of all viral reads. Discussion Viral co-infections are a leading cause of mortality in dogs, with canine parvovirus enteritis often complicated by other pathogens such as canine distemper virus, canine coronavirus, and rotavirus. The presence of multiple pathogens can obscure the primary etiology, highlighting the need for comprehensive molecular diagnostics. Our findings underscore the critical importance of advanced molecular diagnostics in resolving complex infectious disease outbreaks in canine populations and inform future strategies for outbreak prevention and control.