Discovery, phylogenetic, and comparative genomic analysis of novel avian gammacoronaviruses identified in feral pigeons ( Columba livia domestica )

Abstract

Although coronaviruses are significant pathogens affecting a wide range of hosts, surveillance efforts have predominantly focused on wild mammals, leaving the diversity of avian coronaviruses largely underexplored. Here, we report the detection of novel gammacoronaviruses from feral pigeons in South Africa and propose revisions to the current taxonomic classification of Gammacoronavirus based on genetic distance analyses. These findings highlight the potential role of wild birds in the dissemination of novel coronaviruses, analogous to their established involvement in the transmission of avian influenza viruses. Our study also highlights the utility of next-generation sequencing (NGS) technologies in uncovering the hidden diversity of viruses in wildlife populations. Finally, this study reinforces the need for ongoing surveillance, continued vigilance, and further research into avian coronaviruses. The ongoing highly pathogenic avian influenza (HPAI) outbreaks in the USA have demonstrated the devastating impact of emerging avian viruses on wildlife, agriculture, and public health. Given the unpredictability of coronavirus evolution, failing to monitor their diversity and potential for cross-species transmission risks leaving us unprepared for future outbreaks. This study reinforces the urgent need for proactive, large-scale genomic surveillance of wildlife reservoirs to identify emerging CoVs before they become significant threats to animal and human populations.