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

The COVID-19 pandemic caused by SARS-CoV-2 has intensified efforts to identify emerging coronaviruses (CoVs) across diverse hosts. Spillover events, where CoVs transition from wildlife reservoirs to other species, can lead to infections with varying clinical outcomes, emphasizing the need for continued surveillance. Understanding the diversity and distribution of both known and novel CoVs in wildlife reservoirs is crucial for predicting and preventing future spillover events. In this study, we employed Illumina's Pan-CoV library panel and next-generation sequencing (NGS) to identify five novel avian-associated gammacoronavirus genomes from cloacal and oropharyngeal swabs of clinically healthy feral pigeons captured in Durban, KwaZulu-Natal Province, South Africa, in 2018. The genome sequences, ranging from 27,582 to 27,611 nucleotides, clustered with gammacoronaviruses in phylogenetic analyses but formed a distinct clade. Comparative analysis of the five conserved domains in the ORF1ab coding sequence with other gammacoronaviruses revealed Pairwise Patristic Distances (PPD) that exceeded both species and subgenus demarcation cutoffs. These findings highlight the critical need for ongoing surveillance to enhance understanding of CoV diversity, host range, and potential for cross-species transmission, aligning with One Health principles. Based on these results, we propose