Abstract
A new strain of avian paramyxovirus type 6 (APMV-6), JL, has been isolated from mallard ducks in China, and its complete genome has been sequenced and analyzed. This work is the first announced complete genome sequence of APMV-6 from mallards.
GENOME ANNOUNCEMENT
Members of the family Paramyxoviridae are enveloped, negative-stranded RNA viruses that infect a great variety of mammalian and avian species (4). Avian paramyxoviruses are classified in the genus Avulavirus of the subfamily Paramyxovirinae, family Paramyxoviridae (6). There are 11 serotypes (APMV-1 to APMV-11) of APMVs described (1, 2, 5) based on hemagglutination inhibition (HI). Newcastle disease induced by APMV-1 is one of the most serious diseases in poultry; APMV-2, APMV-3, and APMV-6 might also cause severe disease and a drop in egg production in turkeys (6). During an influenza virus surveillance program in Jilin province in 2011, a virus causing hemagglutination was isolated from mallard ducks (Anas poecilorhyncha). By specific reverse transcription-PCR (RT-PCR) and hemagglutination inhibition tests, the sample was negative for avian influenza virus (AIV) and Newcastle disease virus (NDV). This virus was shown by electron microscope to be a paramyxovirus. HI tests using reference sera specific for APMV-2, APMV-3, APMV-6, and APMV-7 were carried out, and the results indicated that it belongs to the APMV-6 serotype. Viral RNA was extracted from infected allantoic fluid harvested 3 days postinoculation using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. The first-strand cDNA was synthesized from viral RNA using random primer (TaKaRa). Sixteen pairs of primers were designed from the published APMV-6 strains TW (GenBank accession no. NC003043) and HK (GenBank accession no. EU622637) to amplify most of the JL strain genome except the 3′ and 5′ termini. The sequences of genome termini were determined by rapid amplification of cDNA ends (RACE) by using the 3′-full RACE kit and 5′-full RACE kit (TaKaRa). The PCR products were cloned into the pMD18-T vector (TaKaRa) and sequenced using an ABI 3730XL Sanger-based genetic analyzer. Sequences were compiled using the SeqMan program in Lasergene. The genome length of strain JL is 16,236 nucleotides (nt), which is consistent with lengths of members of class I of APMV-6 (7), following the “rule of six” (3). The genome consists of seven genes in the order 3′-N-P-M-F-SH-HN-L-5′, which is typical of APMV-6. The level of identity of the complete genomic sequence between strain JL and other strains of APMV-6, including strains HK, TW, FE (GenBank accession no. EF569970), and IT4524-2 (GenBank accession no. GQ406232.1), ranged from 70.3% (strain IT4524-2) to 97.3% (strain TW), that of the F gene from 72.3% (strain IT4524-2) to 97.7% (strain TW), and that of the HN gene from 70.6% (strain IT4524-2) to 97.2% (strain TW). Despite the higher level of identity between strains JL and TW than between JL and other strains, JL has the same amino acid sequence functional motifs of NRKSCS in the HN gene and QGDNQ in the L gene as strain HK, whereas the motifs NRKSCN and QGDEQ, respectively, are found in strain TW (7).
The complete sequence of strain JL is meaningful in understanding the molecular characteristics of APMV-6 and also helpful in elucidating the phylogenetic relationships of APMVs.
Nucleotide sequence accession number.
The genome of strain JL has been submitted to GenBank (accession number JX522537).
ACKNOWLEDGMENT
This study was supported by a Fund for Surveillance of Wildlife Diseases from the Forestry Bureau of China (201003).
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