title: Complete genome sequences of avian paramyxovirus serotype 6 prototype strain Hong Kong and a recent novel strain from Italy: evidence for the existence of subgroups within the serotype.
abstract: Complete genome sequences were determined for two strains of avian paramyxovirus serotype 6 (APMV-6): the prototype Hong Kong (HK) strain and a more recent isolate from Italy (IT4524-2). The genome length of strain HK is 16236 nucleotide (nt), which is the same as for the other two APMV-6 strains (FE and TW) that have been reported to date, whereas that of strain IT4524-2 is 16230 nt. The length difference in strain IT4524-2 is due to a 6-nt deletion in the downstream untranslated region of the F gene. All of these viruses follow the "rule of six". Each genome consists of seven genes in the order of 3'N-P-M-F-SH-HN-L5', which differs from other APMV serotypes in containing an additional gene encoding the small hydrophobic (SH) protein. Sequence comparisons revealed that strain IT4524-2 shares an unexpectedly low level of genome nt sequence identity (70%) and aggregate predicted amino acid (aa) sequence identity (79%) with other three strains, which in contrast are more closely related to each other with nt sequence 94-98% nt identity and 90-100% aggregate aa identity. Sequence analysis of the F-SH-HN genome region of two other recent Italian isolates showed that they fall in the HK/FE/TW group. The predicted signal peptide of IT4524-2 F protein lacks the N-terminal first 10 aa that are present in the other five strains. Also, the F protein cleavage site of strain IT4524-2, REPR downward arrow L, has two dibasic aa (arginine, R) compared to the monobasic F protein cleavage site of PEPR downward arrow L in the other strains. Reciprocal cross-hemagglutination inhibition (HI) assays using post-infection chicken sera indicated that strain IT4524-2 is antigenically related to the other APMV-6 strains, but with 4- to 8-fold lower HI tiers for the test sera between strain IT4524-2 and the other APMV-6 strains. Taken together, our results indicated that the APMV-6 strains represents a single serotype with two subgroups that differ substantially based on nt and aa sequences and can be distinguished by HI assay.
authors.affiliation: Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA.
authors.forename: Sa
authors.initials: S
authors.lastname: Xiao
authors.forename: Madhuri
authors.initials: M
authors.lastname: Subbiah
authors.forename: Sachin
authors.initials: S
authors.lastname: Kumar
authors.forename: Roberta
authors.initials: R
authors.lastname: De Nardi
authors.forename: Calogero
authors.initials: C
authors.lastname: Terregino
authors.forename: Peter L
authors.initials: PL
authors.lastname: Collins
authors.forename: Siba K
authors.initials: SK
authors.lastname: Samal
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000914:Antibodies, Viral / Q000276:immunology; D018109:Avulavirus / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification; D002645:Chickens; D016000:Cluster Analysis; D004372:Ducks; D023061:Gene Order; D005814:Genes, Viral; D016679:Genome, Viral; D006385:Hemagglutination Inhibition Tests; D006723:Hong Kong; D007558:Italy; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D012703:Serotyping; D026801:Synteny
chemical_list: D000914:Antibodies, Viral; D012367:RNA, Viral