A recombinant infectious bronchitis virus from a chicken with a spike gene closely related to that of a turkey coronavirus

Abstract

Using viral metagenomics, the complete genome sequence of an infectious bronchitis virus (IBV) strain (named ahysx-1) from a fecal sample from a healthy chicken in Anhui province, China, was determined. The genome sequence of ahysx-1 was found to be very similar to that of IBV strain ck/CH/LLN/131040 (KX252787), except for the spike gene region, which is similar to that of a turkey coronavirus strain (EU022526), suggesting that ahysx-1 is a recombinant. Recombination analysis and phylogenetic analysis based on the genomic sequences of ahysx-1 and other related strains confirmed that ahysx-1 appears to be a recombinant resulting from a recombination event that occurred between a chicken coronavirus and a turkey coronavirus. Further studies need to be performed to determine whether this recombinant IBV strain is pathogenic and whether it is transmitted between chickens and turkeys. Keywords Viral metagenomics · Coronavirus · Infectious bronchitis virus · Genome recombinationCoronaviruses (CoVs) are enveloped positive-sense RNA viruses that belong to the family Coronaviridae. They have been found in a wide variety of animals and can cause respiratory, enteric, hepatic and neurological diseases [1,2].

The immune response and immune evasion characteristics in SARS-CoV, MERS-CoV, and SARS-CoV-2: Vaccine design strategies

“…Coronaviruses, as known as zoonotic pathogens, belong to the Coronaviridae family of the order Nidovirales. The Coronavirus genome consists of a single‐stranded positive‐sense RNA (+ssRNA) (∼30 kb) that is linked with a 3′poly-A tail (crown-shape peplomers with 80-160 nM in size) and a structure of 5′‐terminal cap [29] . Coronaviruses have the largest genomes (26.4e31.7 kb) among all known RNA viruses.…”

Pathology of Coronavirus Infections: A Review of Lesions in Animals in the One-Health Perspective

“…In 2008, the genome of a CoV causing severe enteritis in turkeys was sequenced [ 268 ] and its origin was ascribed probably to a mutation of the IBV of chickens [ 269 ] that allowed the virus to acquire tropism for the intestinal tract. Additionally, a recombinant strain of IBV with TCoV has been recently identified [ 270 ].…”

Fecal, oral, blood and skin virome of laboratory rabbits

“…Trees based on different regions of the genome of RabPyV showed discordant results, suggesting that this novel rabbit polyomavirus had undergone genetic recombination. To determine whether RabPyV is a recombinant, the complete genome sequences of CPyV (DQ192570), GHPV (AY140984), PPyV (DQ192571), CommonPyV (NC_028119), and BankPyV (KR612372) were aligned with that of RabPyV using CLUSTAL X, and recombination analysis was performed using the Recombination Detection Program 4.0 (RDP 4.0), which includes seven different methods: RDP, GENECONV, BootScan, MaxChi, Chimaera, SiSCan and 3Seq [28]. The results of a manual bootscan analysis suggested that RabPyV resulted from a recombinant event occurring between the major parent NC_028119 and the minor parent DQ192570, with a high degree of confidence (P = 3.662 × 10 −6 ).…”

“…The untranslated regions (UTRs) at the 5′ and 3′ ends usually contain structural elements and are related to replication and/or translation. The replicase gene, which occupies the 5′ two thirds of the CoV genome encodes the non-structural proteins, and the remaining one third encodes four major structural proteins, including the spike (S), membrane (M), envelope (E) and nucleocapsid (N) proteins [28,40]. CoVs are classified into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus.…”