Complete Genome Sequence of an Amur Virus Isolated from Apodemus peninsulae in Northeastern China

Abstract

Amur virus was recently identified as the causative agent of hemorrhagic fever with renal syndrome. Here we report the complete genome sequence of an Amur virus isolated from Apodemus peninsulae in Northeastern China. The sequence information provided here is critical for the molecular epidemiology and evolution of Amur virus in China.

GENOME ANNOUNCEMENT

Hantaviruses within the genus Hantavirus of the family Bunyaviridae cause hemorrhagic fever with renal syndrome (HFRS) in Eurasia and hantavirus pulmonary syndrome (HPS) in the Americas (3). The viruses are commonly maintained within specific rodent hosts, and human infections occasionally occur through inhalation of aerosolized excreta from infected animals. Recently, Amur virus (AMRV) was identified as one of the causative agents of HFRS in Far East Russia and East Asia (4, 6, 10), together with Hantaan, Seoul, Dobrava-Belgrade, and Puumala viruses (1, 2). HFRS is endemic to many provinces in mainland China (7), and AMRV has been reported in China (2, 9). However, no complete genome sequence of Chinese AMRV has ever been reported.

Here we report the complete genome of the Chinese AMRV strain ApJLCB2011. The virus was isolated from the lung tissue of Apodemus peninsulae in Changbai county, Jilin province, China. Total RNA was extracted from virus-infected Vero E6 cells with a QIAamp viral RNA minikit. cDNA synthesis and amplification of complete S, L, and M genomic segments by PCR analysis were carried out as previously described (5). The 5′ and 3′ termini of each segment were determined by using rapid amplification of cDNA ends. All sequencing was carried out using an ABI 3730 Sanger-based genetic analyzer, and one contig containing a high-quality trace file was assembled using DNAStar version 7.0.

The genome of AMRV strain ApJLCB2011 composes three negative-stranded RNA segments, referred to as S, M, and L. The S segment is 1,695 nucleotides (nt) in length, containing a 1,290-nt open reading frame (ORF) which encodes the nucleocapsid protein. The M segment of 3,595 nt contains a 3,408-nt ORF encoding the glycoprotein precursor. The L segment of 6,477 nt contains a 6,456-nt ORF, which encodes viral RNA-dependent RNA polymerase. The nucleotide sequences at the 5′ and 3′ termini of each segment are complementary (8). Phylogenetic analysis based on each individual genomic segment was performed by using MEGA 5.05 with the neighbor-joining method, respectively, and the results demonstrated that ApJLCB2011 belongs to AMRV or Soochong virus entities (1). Sequence analysis of S, L, and M segments showed that ApJLCB2011 has 91.1%, 89.4%, and 87.6% nucleotide identities to the AMRV strain AP209 isolated in Russia, respectively. The deduced amino acids (aa) of the G2 regions are methionine at aa 932 and aspartic acid at aa 967, which has been indicated as the signature aa for AMRV (5). Recombination analyses between newly isolated AMRV and other hantaviruses were performed with SimPlot software, and no obvious recombinant event was detected.

HFRS remains endemic in China and many other countries. The etiological agents in hosts and patients continue evolving, and further field and laboratory investigation should be warranted. The sequence information provided here is critical for the molecular epidemiology and phylogenetic evolution of AMRV in China.

Nucleotide sequence accession numbers.

The nucleotide sequence of the genome of AMRV strain ApJLCB2011 has been deposited within the GenBank sequence database under accession numbers JX473002 (L segment), JX473003 (M segment), and JX473004 (S segment).