| Literature DB >> 36175847 |
Xiao Wei1, Biao Meng1,2, Hong Peng1, Yan Li3, Min Liu3, Hairui Si3, Rui Wu4, Hailong Chen4, Ying Bai3, Yan Li3, Qunling Feng5, Changjun Wang6,7, Xiangna Zhao8,9.
Abstract
BACKGROUND: An outbreak of hemorrhagic fever with renal syndrome (HFRS), caused by a Hantavirus, affected nine adult males in the southwest area of Xi'an in November 2020 was analyzed in this study.Entities:
Keywords: Hantaan virus; Hantavirus; Hemorrhagic fever with renal syndrome
Mesh:
Year: 2022 PMID: 36175847 PMCID: PMC9521858 DOI: 10.1186/s12879-022-07744-1
Source DB: PubMed Journal: BMC Infect Dis ISSN: 1471-2334 Impact factor: 3.667
Fig. 1Timeline of relevant exposures and clinical symptoms of the 9 patients with HFRS
Fig. 2Geographical distribution of the nine confirmed HFRS patients at Chang’an district, Xi’an, China
Strains information for sequence analysis in this study
| Group | Strains | Accession no | Host | Country | Province | ||
|---|---|---|---|---|---|---|---|
| S | M | L | |||||
| HTN Viruses | |||||||
| HTNV 1 | AH09 | AF285264 | AF285265 | – | Niviventer niviventer | China | Anhui |
| NC167 | AB027523 | AB027115 | DQ989237 | Niviventer niviventer | China | Anhui | |
| HTNV 2 | B78 | AB027093 | AB027056 | – | Homo sapiens | China | Shandong |
| H5 | AB127996 | AB127993 | – | Homo sapiens | China | Heilongjiang | |
| Liu | AF288649 | AF288648 | – | Homo sapiens | China | Shandong | |
| HTNV 3 | Q7 | AB027095 | AB027058 | – | Apodemus agrarius | China | Guizhou |
| Q20 | AB027096 | AB027059 | – | Apodemus agrarius | China | Guizhou | |
| Q36 | AB027094 | AB027057 | – | Apodemus agrarius | China | Guizhou | |
| HTNV 4 | A16 | AB027099 | AB027063 | – | Apodemus agrarius | China | Shanxi |
| XAHu09066 | JF421284 | – | – | Homo sapiens | China | Xi'an | |
| CA09082007 | HQ834499 | – | – | Apodemus agrarius | China | Xi'an | |
| CA10081206 | HQ834503 | – | – | Apodemus agrarius | China | Xi'an | |
| CGAa31P9 | – | EF990924 | – | Apodemus agrarius | China | Guizhou | |
| CGHu2 | – | EU363819 | – | Homo sapiens | China | Guizhou | |
| CGHu3612 | – | EF990923 | – | Homo sapiens | China | Guizhou | |
| CGHu3614 | – | EF990922 | – | Homo sapiens | China | Guizhou | |
| CGRni1 | – | EU363815 | – | Rattus nitidus | China | Guizhou | |
| Q10 | – | AB027062 | – | Apodemus agrarius | China | Guizhou | |
| Q32 | DQ371906 | Apodemus agrarius | China | Guizhou | |||
| Q37 | – | AB027064 | – | Apodemus agrarius | China | Guizhou | |
| HTNV 5 | 84FLi | AF366568 | AF366569 | AF336826 | Homo sapiens | China | Shanxi |
| Chen4 | AB027101 | – | – | Homo sapiens | China | Anhui | |
| HTNV 6 | Bao14 | AB127998 | AB127995 | – | Apodemus agrarius | China | Heilongjiang |
| HTN261 | AF252259 | – | – | – | China | Heilongjiang | |
| Q33 | AB027065 | Apodemus agrarius | China | Guizhou | |||
| HTNV 7 | 76-118/PRO | KT885049 | KT885048 | KT885047 | Apodemus agrarius | South Korea | – |
| CUMC-B11 | U37768 | U38177 | – | – | South Korea | – | |
| S85-46 | AF288659 | AF288658 | – | Crocidura russula | China | Sichuan | |
| LR1 | AF288294 | AF288293 | AF288292 | Apodemus agrarius | China | – | |
| Aa04-722 | – | – | KU207174 | Apodemus agrarius | South Korea | – | |
| Aa19-57 | – | – | MW796149 | Apodemus agrarius | South Korea | – | |
| Aa16-176 | – | – | MH598473 | Apodemus agrarius | South Korea | – | |
| HTNV 8 | Z10 | NC_006433 | NC_006437 | NC_006435 | Homo sapiens | China | Zhejiang |
| HTNV 9 | A9 | AF329390 | U00150 | AF293665 | Apodemus agrarius | China | Jiangsu |
| Hu | AB027111 | AB027077 | – | Homo sapiens | China | Hubei | |
| Other HTN virus strains of undetermined subtype | |||||||
| TJJ16 | AY839871 | Rattus confucianus | China | Tianjin | |||
| CGAa75 | EU092220 | Apodemus agrarius | China | Guizhou | |||
| CGRn53 | EF990907 | Rattus norvegicus | China | Guizhou | |||
| CGRn93MP8 | EF990905 | Rattus norvegicus | China | Guizhou | |||
| YU61 | AY748308 | China | |||||
| YU62 | AY748309 | China | |||||
| KY | GU140098 | White rat | China | Yunnan | |||
| Z37 | AF187082 | China | Zhejiang | ||||
| Reference strains | |||||||
| ANDV | AH-1 | AF324902 | AF324901 | AF324900 | – | Argentina | – |
| PUUV | P360 | L11347 | L08755 | – | Clethrionomys glareolus | Russia | – |
| SEOV | L99 | AF288299 | AF288298 | AF288297 | Rattus losea | China | Jiangxi |
| ZT10 | AY766368 | China | Zhejiang | ||||
| DOBV | Dobrava-Belgrade | JQ026204 | JQ026205 | JQ026206 | Apodemus flavicollis | Germany | – |
| SNV | NMR-11 | L37904 | L37903 | L37902 | Peromyscus maniculatus | The United States | – |
Fig. 3Phylogenetic trees for hantaviruses based on the sequences of the S, M, L segments at nucleotide level. The identifiers on the right of the figure indicated the subtype of HTNV and the reference viruses, including DOBV (Dobrava/Belgrade virus), SEOV (Seoul virus), PUUV (Puumala virus), ANDV (Andes hantavirus), and SNV (Sin Nombre virus)
Potential recombination event of hv03xa strain
| Recombinant sequence | hv03xa S segment | |
|---|---|---|
| Estimated breakpoint positions | In alignment | 1744–1774 nt |
| In GenBank | 1665–1695 nt | |
| Parental sequences | Major | A9 |
| Minor | ZT10 | |
| RDP | 1.59E-09 | |
| GENECONV | 1.32E-10 | |
| BOOTSCAN | 3.00E-10 | |
| MaxChi | 3.74E-04 | |
| Chimaera | 1.45E-05 | |
| SiScan | 2.16E-08 | |
| 3Seq | 3.42E-08 | |
Fig. 4Recombination analysis of hv03xa strain. The Bootscan plots of S segment was based on a pairwise distance model by the RDP4 algorithm. A Bootscan Support Percent of over 70% (cutoff value) was considered significant. The relative strains in the recombination analysis were HTNV TJJ16, 76-118/PRO, Z10, KY, CGRn53, A9, CGRn93MP8, A16, 84FLi, YU61, YU62, CGHu3614, CGHu3612, CGAa75, CA09082007, CA10081206, XAHu09066, and SEOV L99, ZT10
Fig. 5Antibody response to HV in the confirmed 9 patients at 6 months, and 1 year after infection. The p-value and 95% confidence intervals were presented. Each line represented the titer for a patient