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Complete genome sequences of avian paramyxovirus serotype 2 (APMV-2) strains Bangor, England and Kenya: evidence for the existence of subgroups within serotype 2.

ABSTRACT: The complete consensus genome sequences of avian paramyxovirus (APMV) serotype 2 strains Bangor, England and Kenya were determined and compared with those of APMV-2 prototype strain Yucaipa and other paramyxoviruses. The genome lengths of APMV-2 strains Bangor, England and Kenya are 15,024, 14,904, 14,916 nucleotides (nt), respectively, compared to 14,904 nt for Yucaipa. Each genome consists of six non-overlapping genes in the order of (3)(')N-P/V/W-M-F-HN-L(5'), with a 55-nt leader at the 3' end. The length of the trailer at the 5' end of strain Bangor was 173 nt, compared to 154 nt for strains England, Kenya, and Yucaipa. In general, sequence comparison of APMV-2 strains England and Kenya with strain Yucaipa have 94.5 and 88% nt and 96 and 92% aggregate amino acid (aa) identity, respectively. In contrast, strain Bangor has a much lower percent nt identity (70.4, 69.4, and 70.8%) and aa identity (75.3, 76.2, and 76.3%) with strains Yucaipa, England, and Kenya, respectively. Furthermore, strain Bangor has a single basic aa residue ((101)TLPSAR F(108)) at the fusion protein cleavage site compared to the dibasic aa ((93)DKPASR F(100)) found in those of other three strains. Reciprocal cross-hemagglutination inhibition (HI) and cross-neutralization assays using post-infection chicken sera indicated that strain Bangor is antigenically related to the other APMV-2 strains, but with a 4- to 8-fold difference in homologous versus heterologous HI titer. These differences in antigenic relatedness suggest that these four APMV-2 strains represent a single serotype with two antigenic subgroups, and this is strongly supported by the dimorphism in nt and aa sequence identity.

SUBMITTER: Subbiah M

PROVIDER: S-EPMC2914170 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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Complete genome sequences of avian paramyxovirus serotype 2 (APMV-2) strains Bangor, England and Kenya: evidence for the existence of subgroups within serotype 2.

Subbiah Madhuri M Nayak Shreeraj S Collins Peter L PL Samal Siba K SK

Virus research 20100622 1-2

The complete consensus genome sequences of avian paramyxovirus (APMV) serotype 2 strains Bangor, England and Kenya were determined and compared with those of APMV-2 prototype strain Yucaipa and other paramyxoviruses. The genome lengths of APMV-2 strains Bangor, England and Kenya are 15,024, 14,904, 14,916 nucleotides (nt), respectively, compared to 14,904 nt for Yucaipa. Each genome consists of six non-overlapping genes in the order of (3)(')N-P/V/W-M-F-HN-L(5'), with a 55-nt leader at the 3' en ...[more]

PMID: 20600395

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Project description:BackgroundAvian paramyxoviruses (APMV) consist of nine known serotypes. The genomes of representatives of all APMV serotypes except APMV type 5 have recently been fully sequenced. Here, we report the complete genome sequence of the APMV-5 prototype strain budgerigar/Kunitachi/74.Methodology/principal findingsAPMV-5 Kunitachi virus is unusual in that it lacks a virion hemagglutinin and does not grow in the allantoic cavity of embryonated chicken eggs. However, the virus grew in the amniotic cavity of embryonated chicken eggs and in twelve different established cell lines and two primary cell cultures. The genome is 17,262 nucleotides (nt) long, which is the longest among members of genus Avulavirus, and encodes six non-overlapping genes in the order of 3'N-P/V/W-M-F-HN-L-5' with intergenic regions of 4-57 nt. The genome length follows the 'rule of six' and contains a 55-nt leader sequence at the 3'end and a 552 nt trailer sequence at the 5' end. The phosphoprotein (P) gene contains a conserved RNA editing site and is predicted to encode P, V, and W proteins. The cleavage site of the F protein (G-K-R-K-K-R downward arrowF) conforms to the cleavage site motif of the ubiquitous cellular protease furin. Consistent with this, exogenous protease was not required for virus replication in vitro. However, the intracerebral pathogenicity index of APMV-5 strain Kunitachi in one-day-old chicks was found to be zero, indicating that the virus is avirulent for chickens despite the presence of a polybasic F cleavage site.Conclusions/significancePhylogenetic analysis of the sequences of the APVM-5 genome and proteins versus those of the other APMV serotypes showed that APMV-5 is more closely related to APMV-6 than to the other APMVs. Furthermore, these comparisons provided evidence of extensive genome-wide divergence that supports the classification of the APMVs into nine separate serotypes. The structure of the F cleavage site does not appear to be a reliable indicator of virulence among APMV serotypes 2-9. The availability of sequence information for all known APMV serotypes will facilitate studies in epidemiology and vaccinology.

Project description: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.

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Dataset Information

Complete genome sequences of avian paramyxovirus serotype 2 (APMV-2) strains Bangor, England and Kenya: evidence for the existence of subgroups within serotype 2.

Publications

Complete genome sequences of avian paramyxovirus serotype 2 (APMV-2) strains Bangor, England and Kenya: evidence for the existence of subgroups within serotype 2.

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