Full genome analysis of a novel type II feline coronavirus NTU156

Abstract

Infections by type II feline coronaviruses (FCoVs) have been shown to be significantly correlated with fatal feline infectious peritonitis (FIP). Despite nearly six decades having passed since its first emergence, different studies have shown that type II FCoV represents only a small portion of the total FCoV seropositivity in cats; hence, there is very limited knowledge of the evolution of type II FCoV. To elucidate the correlation between viral emergence and FIP, a local isolate (NTU156) that was derived from a FIP cat was analyzed along with other worldwide strains. Containing an in-frame deletion of 442 nucleotides in open reading frame 3c, the complete genome size of NTU156 (28,897 nucleotides) appears to be the smallest among the known type II feline coronaviruses. Bootscan analysis revealed that NTU156 evolved from two crossover events between type I FCoV and canine coronavirus, with recombination sites located in the RNA-dependent RNA polymerase and M genes. With an exchange of nearly one-third of the genome with other members of alphacoronaviruses, the new emerging virus could gain new antigenicity, posing a threat to cats that either have been infected with a type I virus before or never have been infected with FCoV.

Feline Coronaviruses

“…There is consistent evidence from independent studies that serotype II viruses emerge via double homologous recombination between serotype I FCoV and CCoV Haijema et al, 2007;Herrewegh et al, 1998;Lin et al, 2013;Lorusso et al, 2008;Terada et al, 2014). As a consequence of the recombination, approximately one-third (10 kb) of the serotype I FCoV genome including the S gene and the neighboring regions are replaced with the equivalent parts of the CCoV genome Haijema et al, 2007;Herrewegh et al, 1998;Lin et al, 2013;Lorusso et al, 2008;Terada et al, 2014). Detailed sequence analyses of numerous serotype II FCoVs revealed that the 5 0 -recombination event occurs in the polymerase gene while the 3 0 -recombination site is located in the E or M genes.…”

“…Furthermore, serotype II FCoVs have predominantly been observed in Asia and they were reported to be responsible for up to 25% of the natural infections in those countries (Amer et al, 2012;An et al, 2011;Sharif et al, 2010). There is consistent evidence from independent studies that serotype II viruses emerge via double homologous recombination between serotype I FCoV and CCoV Haijema et al, 2007;Herrewegh et al, 1998;Lin et al, 2013;Lorusso et al, 2008;Terada et al, 2014). As a consequence of the recombination, approximately one-third (10 kb) of the serotype I FCoV genome including the S gene and the neighboring regions are replaced with the equivalent parts of the CCoV genome Haijema et al, 2007;Herrewegh et al, 1998;Lin et al, 2013;Lorusso et al, 2008;Terada et al, 2014).…”

“…Detailed sequence analyses of numerous serotype II FCoVs revealed that the 5 0 -recombination event occurs in the polymerase gene while the 3 0 -recombination site is located in the E or M genes. However, the exact locations of these recombination sites vary in the different isolates, indicating that serotype II FCoVs continuously arise through independent recombination events (Haijema et al, 2007;Herrewegh et al, 1998;Lin et al, 2013;Terada et al, 2014). It is considered likely that the described recombination occurs in cats that are coinfected with serotype I FCoV and CCoV.…”

“…However, the exact source of serotype II FCoVs is unclear. It is believed that serotype II FCoVs are more virulent (Lin et al, 2013;Wang et al, 2013).…”

In silico and in vitro analysis of small molecules and natural compounds targeting the 3CL protease of feline infectious peritonitis virus

“…The genome of FIPV contains a positive-sense, single-stranded RNA that is approximately 29,000 nucleotides in length, with 11 open reading frames (ORFs) encoding structural, non-structural, and accessory genes (Pedersen, 2009(Pedersen, , 2014aLin et al, 2013). Two-thirds of the FCoV genome at the 5' end comprise two overlapping ORFs, ORF1a and 1b, which encode two polyproteins.…”