Epidemic Trend and Molecular Evolution of HV Family in the Main Hantavirus Epidemic Areas From 2004 to 2016, in P.R. China

Abstract

Hemorrhagic fever with renal syndrome (HFRS) is caused by hantavirus (HV) infection, and is prevalent across Europe and Asia (mainly China). The genetic variation and wide host range of the HV family may lead to vaccine failure. In this study, we analyzed the gene sequences of HV isolated from different regions of China in order to trace the molecular evolution of HV and the epidemiological trends of HFRS. A total of 16,6975 HFRS cases and 1,689 HFRS-related deaths were reported from 2004 to 2016, with the average annual incidence rate of 0.9674 per 100,000, 0.0098 per 100,000 mortality rate, and case fatality rate 0.99%. The highest number of cases were detected in 2004 (25,041), and after decreasing to the lowest numbers (8,745) in 2009, showed an incline from 2010. The incidence of HFRS is the highest in spring and winter, and three times as many men are affected as women. In addition, farmers account for the largest proportion of all cases. The main hosts of HV are Rattus norvegicus and Apodemus agrarius, and the SEOV strain is mainly found in R. norvegicus and Niviventer confucianus. Phylogenetic analysis showed that at least 10 HTNV subtypes and 6 SEOV subtypes are endemic to China. We found that the clustering pattern of M genome segments was different from that of the S segments, indicating the possibility of gene recombination across HV strains. The recent increase in the incidence of HFRS may be related to climatic factors, such as temperature, relative humidity and hours of sunshine, as well as biological factors like rodent density, virus load in rodents and genetic variation. The scope of vaccine application should be continuously expanded, and surveillance measures and prevention and control strategies should be improved to reduce HFRS infection in China.

Keywords: epidemical tendency; genetic variation; hantavirus; incidence rate; molecular evolution.

Figure 1

Annual average incidence of hemorrhagic fever with renal syndrome (HFRS) in provinces across China from 2004 to 2016. According to the average annual incidence rate, the regions in China were divided into four categories: low epidemic – 0–0.01/10,0000; moderate endemic - 0.01–1/10,0000; high-endemic – 1–5/10,0000; very highly endemic > 5/10,0000. Heilongjiang was classified as a highly endemic area and Shaanxi, Jilin, Liaoning, Shandong, Hebei, Jiangxi and Zhejiang. Xinjiang is a low-endemic area. All other areas are considered moderately endemic.

Figure 2

Quarterly distribution of hantavirus (HV) cases in several provinces with severe epidemics. From 2004 to 2016, the incidence of HFRS in each province showed an overall downward trend. (A) The seasonal trends of hemorrhagic fever with renal syndrome (HFRS) incidence throughout the country shows summer and autumn/winter peaks, and the autumn peak is higher. (B–E) Bimodal seasonal peaks in Jiangxi, Fujian, Zhejiang and Jiangsu provinces in Southeast China. (F–K) HFRS initially occurred in colder months in the Shaanxi, Liaoning, Jilin, Heilongjiang, Hebei, and Shandong provinces in North China, but the recent trend is bimodal. (L) shows the legend used by (A–K).

Figure 3

Age, gender, and occupational distribution of hemorrhagic fever with renal syndrome (HFRS) cases. (A, B) HFRS cases in the different age- and gender groups between 2004 and 2016. The 15–64 age group and males were predominantly affected. (C) Occupation of HFRS patients. Farmers are the main affected population.

Figure 4

The distribution of hantavirus (HV) genotypes across different regions. HTNV and SEOV were predominant in most provinces. There were three distinct genotypes in Jiangxi and Zhejiang respectively. The main genotypes in Guangxi and Xinjiang were Xuan son, LAIBIN, and TULA.

Figure 5

The hantavirus (HV) M segment sequence homology analysis in China. The upper triangle region represents the nucleotide sequence homology and the lower triangle region indicates amino acid homology. The nucleotide and amino acid homology between HTNV strains in Jiangsu Province were 84.6% and 95.4%. The nucleotide and amino acid homology of HTNV strains in Zhejiang Province were 86.5%–99.8% and 96.8%–99.6%, and of SEOV were 83.8%–99.7% and 96.4%–99.5% respectively. The Yuhuan-Sm-1011 strain is a new genotype distinct from HTNV and SEOV.

Figure 6

The hantavirus (HV) S segment sequence homology analysis in China. The upper triangle region represents the nucleotide sequence homology and the lower triangle region indicates amino acid homology. There was 77%–99% nucleotide homology and 91%–99% amino acid homology between HTNV strains in Anhui province. The nucleotide and amino acid homology of HTNV strains in Jiangxi Province were 94.6%–100% and 98.6%–100%, and of SEOV were 88%–99.5% and 98.6%–99.1% respectively.

Figure 7

Phylogenetic tree of hantavirus (HV)-based on the open reading frame of M segments sequence. The tree was constructed by the maximum likelihood method (ML) of Mega software. A new HV type was identified if the nucleotide sequence of at least one fragment was >25% different from other known HV sequences, and a new subtype was the result of 5% sequence difference. Accordingly, nine subtypes were identified for HTNV and five for SEOV. Nucleic acid sequence difference < 5% indicated the same subtype. Subtypes H7 and H8 were mainly found in the southeast coastal areas. The GenBank accession numbers of the viruses are shown in Table S1 .

Figure 8

Phylogenetic tree (ML) of HV-based on the open reading frame of S segments sequence. SEOV is widely distributed in China, and the subtypes of SEOV in the southeast coastal areas are mainly S1 and S3. The GenBank accession numbers of the viruses is shown in Table S1 .

Figure 9

The re-assortment analysis of complete sequences of hemorrhagic fever with renal syndrome (HFRS). (A) The M segment re-assortment of A16 virus strain. The assortment of the H8205 and SN7 virus strain. The recombination breakpoint is 2,214–3,408 bp, which indicates that hantavirus (HV) with the same subtype and similar host is more likely to undergo gene recombination. (B) The re-assortment analysis of CGRn2616 and CGAa4P15 based on the S segment, indicating no gene assortment.