Abstract

The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in chickens and ducks using a conserved RT-PCR assay. The viral genome harbors a tandem repeat which is rare in vertebrate RNA viruses. The repeat is homologous to some proteins of various cellular organisms, but its origin remains unknown. Many substitutions, insertions, deletions, and some frameshifts and recombination events have occurred in the genome of the DdCoV, as compared with the coronavirus dominant in chickens (CdCoV). The distances between DdCoV and CdCoV are large enough to separate them into different species within the genus Gammacoronavirus. Our surveillance demonstrated that DdCoVs and CdCoVs belong to different lineages and occupy different ecological niches, further supporting that they should be classified into different species. Our surveillance also demonstrated that DdCoVs and CdCoVs are prevalent in live poultry markets in some regions of China. In conclusion, this study shed novel insight into the genetic diversity, evolution, distribution, and taxonomy of the coronaviruses circulating in chickens and ducks.

Highlights

  • The severe acute respiratory syndrome (SARS) epidemic in 2003 which resulted in 775 human deaths was caused by SARS coronavirus (CoV) [1,2]

  • We sequenced the whole genome of duck-dominant CoV (DdCoV)/GD/2014 except approximately 170–180 nucleotides at the 50 non-coding region (NCR) and some adenosines at the 30 ploy(A) tail

  • The tandem repeats in both DdCoVs and HKU1 CoVs are located at highly variable regions in the PL1pro domain of nsp3

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Summary

Introduction

The severe acute respiratory syndrome (SARS) epidemic in 2003 which resulted in 775 human deaths was caused by SARS coronavirus (CoV) [1,2]. The ongoing Middle East respiratory syndrome (MERS) infections in recent years which have claimed hundreds of human lives were caused by MERS CoV [3]. The discovery of these two previously unknown CoVs and other CoVs related to them in animals has greatly broadened our knowledge about the distribution, diversity, and significance of CoVs in both humans and animals [3,4,5,6,7].

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