Molecular diversity of Alphacoronavirus 1 in dogs and cats in Colombia

N.F Santana-Clavijo,D.P Reyes Romero,D.F Arango Fajardo,A Velandia Muñoz,S.A Taniwaki,S.O De Souza Silva,P.E Brandão

doi:10.1016/j.heliyon.2020.e04381

Abstract

Alphacoronavirus 1 (subgenus Tegacovirus, genus Alphacoronavirus, family Coronaviridae), which encompasses transmissible gastroenteritis virus (TGEV), feline coronavirus (FCoV) and canine coronavirus (CCoV), is an important pathogen that can cause severe gastroenteritis and is distributed worldwide. CCoV has two different genotypes: CCoV type I, which has a high identity with FCoV-I, and CCoV type II, which is divided into two subtypes, CCoV IIa (pantropic) and CCoV IIb, which is related to FCoV-II and has been involved in multiple recombination events. Between 2014 and 2018, 43 fecal samples from puppies and young dogs under 1 year of age with hemorrhagic enteritis and from 5 cats under 2 years of age with ascites or thoracic effusion were collected by a private veterinary practice in Bogotá, Colombia. A screening for Coronavirus via RT-PCR (nsp12) and PCR amplification of Canine protoparvovirus (VP1) revealed 27.1% (13/49) and 72.9% (35/49) positive samples, respectively. Positive samples for coronavirus were tested for M, N, S and the sequences grouped in the FCoV, CCoV-I and CCoV-IIb clusters that were distant from the pantropic type (IIa). The N gene formed two clusters, one exclusively with samples from this study in subtype II and another with strains in subtype I. For gene S (subtype I), the samples clustered with the Brazilian samples, while samples positive for S subtype IIb grouped into a cluster distinct from the other reference sequences. The prevalence of coronaviruses identified in this study is within the range reported by different countries worldwide.

Highlights

Alphacoronavirus 1 (Nidovirales: Coronaviridae: Coronavirinae: Alphacoronavirus: Tegacovirus) is a large enveloped virus species with a singlestranded positive-sense RNA genome that is 29 kb in size (Decaro et al, 2015), and this virus can infect dogs, cats and pigs
This paper reports on the previously unknown molecular diversity of Alphacoronavirus 1 in cats and dogs in Colombia to provide phylogenetic information regarding this virus species in South America
For the N gene, one sample from a dog resulted in a sequence typed as the canine coronavirus (CCoV)-I H717716 sample, which clustered closely to CCoV-I strains detected in Brazil in 2009 (KP322089.1) and in Italy in 2003 (AY548235.1), while three sequences were found to be related to CCoVII MH717718 and MH717717 in one subcluster and MH795528 in a second subcluster, each of which was distinct from the pantropic CCoV type (DQ112226.1)

Summary

Introduction

Alphacoronavirus 1 (Nidovirales: Coronaviridae: Coronavirinae: Alphacoronavirus: Tegacovirus) is a large enveloped virus species with a singlestranded positive-sense RNA genome that is 29 kb in size (Decaro et al, 2015), and this virus can infect dogs, cats and pigs. Located downstream of ORF1b are up to 11 ORFs that encode the 4 structural proteins spike glycoprotein (S), membrane (M), envelope (E) and nucleocapsid (N) and a variable set of accessory proteins (3a, 3b, 3c, 7a and 7b) (Decaro and Buonavoglia, 2011). Alphacoronavirus 1 encompasses the host-type species canine coronavirus (CCoV), feline coronavirus (FCoV), transmissible gastroenteritis virus (TGEV) and porcine respiratory virus (PRCoV) (Decaro and Buonavoglia, 2011; Ntafis et al, 2013). Kitts (De Barros et al, 2018; Decaro et al, 2010; Navarro et al, 2017; Ntafis et al, 2013; Pinto et al, 2014; Soma et al, 2011; Zicola et al, 2012)

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