ABSTRACT
Although rodents are important reservoirs for RNA viruses, to date only one species of rodent coronavirus (CoV) has been identified. Herein, we describe a new CoV, denoted Lucheng Rn rat coronavirus (LRNV), and novel variants of two Betacoronavirus species termed Longquan Aa mouse coronavirus (LAMV) and Longquan Rl rat coronavirus (LRLV), that were identified in a survey of 1465 rodents sampled in China during 2011-2013. Phylogenetic analysis revealed that LAMV and LRLV fell into lineage A of the genus Betacoronavirus, which included CoVs discovered in humans and domestic and wild animals. In contrast, LRNV harbored by Rattus norvegicus formed a distinct lineage within the genus Alphacoronavirus in the 3CL(pro), RdRp, and Hel gene trees, but formed a more divergent lineage in the N and S gene trees, indicative of a recombinant origin. Additional recombination events were identified in LRLV. Together, these data suggest that rodents may carry additional unrecognized CoVs.
Subject(s)
Coronavirus/genetics , Coronavirus/isolation & purification , Rodentia/virology , Animals , China , Coronavirus/classification , Coronavirus, Rat/classification , Coronavirus, Rat/genetics , Coronavirus, Rat/isolation & purification , Disease Reservoirs/virology , Evolution, Molecular , Genetic Variation , Genome, Viral , Humans , Mice , Molecular Sequence Data , Phylogeny , Rats , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/geneticsABSTRACT
BACKGROUND: Longquan City, Zhejiang province, China, has been seriously affected by hemorrhagic fever with renal syndrome (HFRS) since the first cases were registered in 1974. To understand the epidemiology and emergence of HFRS in Longquan, which may be indicative of large parts of rural China, we studied long-term incidence patterns and performed a molecular epidemiological investigation of the causative hantaviruses in human and rodent populations. METHOD/PRINCIPAL FINDINGS: During 1974-2011, 1866 cases of HFRS were recorded in Longquan, including 20 deaths. In 2011, the incidence of HFRS remained high, with 19.61 cases/100,000 population, despite the onset of vaccination in 1997. During 1974-1998, HFRS cases in Longquan occurred mainly in winter, while in the past decade the peak of HFRS has shifted to the spring. Notably, the concurrent prevalence of rodent-borne hantaviruses in the region was also high. Phylogenetic analyses of viral sequences recovered from rodents in Longquan revealed the presence of novel genetic variants of Gou virus (GOUV) in Rattus sp. rats and Hantaan virus (HTNV) in the stripe field mice, respectively. Strikingly, viral sequences sampled from infected humans were very closely related to those from rodents. CONCLUSIONS/SIGNIFICANCE: HFRS represents an important public health problem in Longquan even after years of preventive measures. Our data suggest that continual spillover of the novel genetic variant of GOUV and the new genetic lineage of HTNV are responsible for the high prevalence of HFRS in humans. In addition, this is the first report of GOUV associated with human HFRS cases, and our data suggest that GOUV is now the major cause of HFRS in this region.
Subject(s)
Hemorrhagic Fever with Renal Syndrome/epidemiology , Hemorrhagic Fever with Renal Syndrome/veterinary , Orthohantavirus/classification , Orthohantavirus/isolation & purification , Rodent Diseases/epidemiology , Zoonoses/epidemiology , Zoonoses/virology , Animals , China/epidemiology , Cluster Analysis , Orthohantavirus/genetics , Hemorrhagic Fever with Renal Syndrome/virology , Humans , Incidence , Mice , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , Prevalence , RNA, Viral/genetics , Rats , Rodent Diseases/virology , Seasons , Sequence Analysis, DNAABSTRACT
OBJECTIVE: To investigate the situation of the natural infection of hantaviruses (HV) in small mammals and to provide evidence for the control and prevention of hemorrhagic fever with renal syndrome (HFRS) in Longquan area, Zhejiang province. METHODS: Small mammals were captured by night trap, and lung tissue samples were collected and stored in liquid nitrogen. HV antigens were detected by indirect immuno-fluorescence assay (IFA). The partial S genome segment sequences were amplified by RT-PCR. DNAStar program was used for editing and comparing the sequences. Phylogeny was analyzed through PAUP*4.0 software. RESULTS: 319 small animals were collected in Longquan, and 9 hantavirus antigen-positive samples were identified. The positive rate of hantavirus in Apodemus agrarius was 4.97%. Phylogenetic tree constructed by partial S segment (620 - 999 nt) showed that the 9 strains carried by A. agrarius from Longquan all belonged to HTNV, and had a closer evolutionary relationship with isolate Z251 from Zhejiang province. CONCLUSION: Our results indicated that the main host was A. agrarius and the infection rate of HTNV was high in Longquan area.
