Emergence of Avian coronavirus genotype GI-11 in Colombia
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VETERINARY MICROBIOLOGY - SHORT COMMUNICATION
Emergence of Avian coronavirus genotype GI-11 in Colombia Nelson F. Santana-Clavijo 1
&
Paulo E. Brandão 1
Received: 8 June 2020 / Accepted: 17 October 2020 # Sociedade Brasileira de Microbiologia 2020
Abstract Avian coronavirus (AvCoV/IBV) is a virus with high morbidity, which can cause respiratory, digestive, renal, and reproductive diseases in chickens. Molecular detection and sequencing are the main tool for identification and classification of AvCoV. Thirtysix samples were collected in three broiler farms from different regions in Colombia, due to mortality increase; ten samples were positive using RT-qPCR targeted to the 5′ UTR of AvCoV, and one sample was positive and had its partial S gene sequenced. Phylogenetic analysis revealed that this strain belongs to the GI-11 lineage, similar to the Brazilian cluster. Several lineages have already been described in Colombia but, to the best of our knowledge, this is the first time that GI-11 has been detected in this country, which suggests that this subtype may be more widespread in South America than previously thought. Keywords Avian coronavirus . Subtype GI-11 . Morbidity . Phylogenetic analyses . Brazilian cluster
Avian coronavirus (AvCoV, host-type avian infectious bronchitis virus, IBV) is the causative agent of highly contagious diseases for chickens, placing a significant economic burden on the poultry industry worldwide [9, 12]. AvCoV belongs to order Nidovirales, family Coronaviridae, subfamily Orthocoronavirinae, genus Gammacoronavirus, and subgenus Igacovirus [16]. The viral genome is single-stranded RNA, positive sense, with 30 kb, which comprises two untranslated regions (UTRs) at the 5′ and 3′ ends [19, 28], two overlapping open read frames (ORFs) encoding the polyproteins 1a and 1ab (15 nonstructural proteins), and eight ORFs that codes for structural proteins (S, E, M, N) and accessory proteins (3a, 3b, 5a, 5b) [7, 23]. The spike protein is a glycoprotein responsible for binding to host receptors and determines the tropism and host range of the virus [30]; this glycoprotein has two subunits, S1 that is anchored to viral membrane by S2 subunit [1]. Subunit S1 contains the epitopes involved in the induction of serotypespecific neutralizing antibodies, but cross protection is poor Responsible Editor: Fernando R. Spilki. * Nelson F. Santana-Clavijo [email protected] 1
Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, Professor Doutor Orlando Marques de Paiva, 87, São Paulo, SP 05508-270, Brazil
and most of these serotypes differ from each other by 20–25% at amino acid level in S1 subunit [1, 26, 29]. Nucleotide heterogenicity is more prevalent in the S1 portion of the S gene and is largely contained in three different hypervariable regions (HVR) (aa 38–67, 91–141, 275–287). The analysis of complete or partial S1 gene nucleotide sequence has been conventionally used to determinate viral genetic types, and more than 50 different a
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