Molecular Characterization of Infectious Bronchitis Virus Strain HH06 Isolated in a Poultry Farm in Northeastern China.

Ghulam Abbas,Xiaodan Huang,Yue Zhang,Xiaowei Sun,Yudong Ren,Xiurong Wang,Huijie Chen,Guangxing Li,Muhammad Zulfiqar Ahmad

doi:10.3389/fvets.2021.794228

Abstract

Spike (S) glycoprotein is an important virulent factor for coronaviruses (CoVs), and variants of CoVs have been characterized based on S gene analysis. We present phylogenetic relationship of an isolated infectious bronchitis virus (IBV) strain with reference to the available genome and protein sequences based on network, multiple sequence, selection pressure, and evolutionary fingerprinting analysis in People's Republic of China. One hundred and elven strains of CoVs i.e., Alphacoronaviruses (Alpha-CoVs; n = 12), Betacoronaviruses (Beta-CoVs; n = 37), Gammacoronaviruses (Gamma-CoVs; n = 46), and Deltacoronaviruses (Delta-CoVs; n = 16) were selected for this purpose. Phylogenetically, SARS-CoV-2 and SARS-CoVs clustered together with Bat-CoVs and MERS-CoV of Beta-CoVs (C). The IBV HH06 of Avian-CoVs was closely related to Duck-CoV and partridge S14, LDT3 (teal and chicken host). Beluga whale-CoV (SW1) and Bottlenose dolphin-CoVs of mammalian origin branched distantly from other animal origin viruses, however, making group with Avian-CoVs altogether into Gamma-CoVs. The motif analysis indicated well-conserved domains on S protein, which were similar within the same phylogenetic class and but variable at different domains of different origins. Recombination network tree indicated SARS-CoV-2, SARS-CoV, and Bat-CoVs, although branched differently, shared common clades. The MERS-CoVs of camel and human origin spread branched into a different clade, however, was closely associated closely with SARS-CoV-2, SARS-CoV, and Bat-CoVs. Whereas, HCoV-OC43 has human origin and branched together with bovine CoVs with but significant distant from other CoVs like SARS CoV-2 and SARS-CoV of human origin. These findings explain that CoVs' constant genetic recombination and evolutionary process that might maintain them as a potential veterinary and human epidemic threat.

Highlights

Coronaviruses (CoVs) are a group of RNA viruses that mainly infect respiratory systems of domestic and wild birds as well as mammals including humans
Difference of amino acids in S1 by 20∼50% is considered for different serotypes, in some instances, only 2% or 10∼15 amino acids variation may lead to the emerging of different serotypes of infectious bronchitis virus (IBV) [10, 11]
Among selected viruses were SARS-CoV2, SARS-CoV, and Middle East Respiratory Syndrome (MERS)-CoV of mammalian origin along with IBV strain HH06 of avian origin isolated in this study

Summary

Introduction

Coronaviruses (CoVs) are a group of RNA viruses that mainly infect respiratory systems of domestic and wild birds as well as mammals including humans. These viruses belong to the subfamily Orthocoronavirinae of the family Coronaviridae [1, 2], further classified into Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus genera [3]. Evolution process is considered important factor which plays major role in many emerging serotypes. Indicating the positions of amino acids evolutionary conservation is important for maintaining the protein structure and function [12, 13]. Detection of selected sites may enlighten the selection forces and detects the functionally significant sites for CoVs S protein interaction

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Conclusion