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

Abstract

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 Gammacoronavirus columbae as a new species for these pigeon gammacoronaviruses that clusters with the recently reported duck gammacoronaviruses to form a novel subgenus within Gammacoronavirus.IMPORTANCEAlthough 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.

Keywords: Columba livia domestica; avian; coronavirus; evolution; feral pigeons; gammacoronaviruses; genome sequence; next-generation sequencing; pan-coronavirus.