Genetic and hosts characterization of hantaviruses in port areas in Hainan Province, P. R. China

Abstract

Background: Hantaviruses (HVs) are major zoonotic pathogens in China that cause hemorrhagic fever with renal syndrome (HFRS) posing a major threat to people's health. Hainan Province, an island located in Southeast China, is an ideal region for sea ports. The unique tropical monsoon climate in Hainan provides sufficient living conditions for rodents, which help spread HVs and other rodent-borne diseases. In the routine monitoring of hantavirus, there was no evidence that rodents in Hainan carried hantavirus. No patients infected with hantavirus were found in the past. However, the surveillance of HVs-carrying rodents covering the whole territory of Hainan has not stopped.

Methodology/principal findings: For the monitoring of the prevalence of HVs in rodents and the search for theoretical reference for rodent control and HFRS prevention, a total of 60 rodents from 6 monitoring spots were trapped around main ports in Hainan between 2016 and 2019. HV positive samples were identified by a specific kit and sequenced. The data indicated that seven rodents (Rattus norvegicus) were positive for hantavirus with a positivity rate of 11.67%. Phylogenetic analysis suggested that the two complete sequence strains HN1 and HN4 in this research were highly similar to the sequence strains GZRn36 and GZRn148 isolated in Guangdong Province, and they located in the same phylogenetic tree branch which belongs to S2 subtype. Although the two partial sequences HT1 and HT2 isolated in Xisha Islands belong to S2 subtype according to the phylogenetic tree of L segment, they showed a great nucleotide difference with HN1 and HN4. We also found 13 amino acid variations compared with SEOV 80-39 and 6 amino acid mutations related to epitope, and the variations may reduce the effectiveness of the current HFRS vaccines used in humans.

Conclusions/significance: The study indicated HVs carried by rodents found in Hainan Province may be transmitted from Guangdong Province through trading ports and carriage of goods by sea. So it is of great significance to strengthen the surveillance of rodents in port areas especially capture and eliminate rodents on ship. Timely elimination of host animals of hantavirus in port areas is necessary to prevent an outbreak of HVs disease.

Fig 1. The sampling cities of rodents in Hainan Province from 2016 to 2019.

A: The map of China. B: The sampling locations in 2016 including Dongfang and Wenchang. C: The sampling locations in 2017 including Dongfang, Danzhou, Haikou and Wenchang. D: The sampling locations in 2018 including Dongfang and Sansha. E: The sampling locations in 2019 including Sansha. Note: The map source referred to maps at the CIA which was similar but not identical to the original image and was therefore for illustrative purposes only.

Fig 2. The positive rate in different cities during 2016–2019.

F: The positive rate of hantavirus in Hainan Province in 2016. G: The positive rate of hantavirus in Hainan Province in 2017. H: The positive rate of hantavirus in Hainan Province in 2018. I: The positive rate of hantavirus in Hainan Province in 2019.

Fig 3. The phylogenetic tree based on ORF of L segment nucleotide sequences of hantavirus in Hainan and others.

According to the phylogenetic analysis, the “L” sequences of the four hantavirus strains sequences found in Hainan Province belong to S2 subtype of SEOV. Note: The small red triangle represents the newly discovered hantavirus sequences in this study.

Fig 4. The phylogenetic tree based on ORF of M segment nucleotide sequences of hantavirus in Hainan and others.

The ‘M’ sequences (named HN1M and HN4M) of the two hantavirus HN1 and HN4 show a close genetic distance with GZRn76, HN71-L, Guang199 and Beijing-Rn, which belong to S2 subtype. Note: The small red triangle represents the newly discovered hantavirus sequences in this study.

Fig 5. The phylogenetic tree based on ORF of S segment of hantavirus nucleotide sequences in Hainan and others.

The HN1 and HN4 are located in the same branch of the phylogenetic tree with GZRn76, GZRn148 and GuangzhouRn36 isolated from Guangzhou. Note: The small red triangle represents the newly discovered hantavirus sequences in this study.

Fig 6. The tertiary structure of glycoprotein based on M segment.

A: The amino acid variation analysis between HN1 and Z37 and L99 with the highest similarity to GC protein. B: The amino acid variation analysis between HN4 and Z37 and L99 with the highest similarity to GC protein.