Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China
ObjectiveWild animal pathogen surveillance will help to understand the next possible pandemic in advance. Rodents, which have close contact with humans, are generally regarded as a key factor for zoonotic disease control. Given the variation in rodent virus composition in diverse ecologies, we condu...
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| Format: | Article |
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.701089/full |
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| author | Teng Zhao Yun-qi Dang Yun-qi Dang Ao-nan Wang Ao-nan Wang He-ting Gao Heng-duan Zhang Dan Xing Bo-qi Li Bo-qi Li Yong-jiu Li Zhu Liu Chun-xiao Li |
| author_facet | Teng Zhao Yun-qi Dang Yun-qi Dang Ao-nan Wang Ao-nan Wang He-ting Gao Heng-duan Zhang Dan Xing Bo-qi Li Bo-qi Li Yong-jiu Li Zhu Liu Chun-xiao Li |
| author_sort | Teng Zhao |
| collection | DOAJ |
| description | ObjectiveWild animal pathogen surveillance will help to understand the next possible pandemic in advance. Rodents, which have close contact with humans, are generally regarded as a key factor for zoonotic disease control. Given the variation in rodent virus composition in diverse ecologies, we conducted a study on the viral infection of rodents of diverse species in different typical environments of Heilongjiang and Yunnan Provinces, located in northeastern and southwestern China, respectively.MethodsViral metagenomics sequencing and bioinformatic analysis were performed to determine the different distributions of rodent-borne viruses in typical environments of Heilongjiang and Yunnan Provinces, China. After viral culture and PCR confirmation, genomic and phylogenetic quantitative analysis was performed on the detected hantaviruses (HVs) and Beilong viruses (BeiVs).ResultsNineteen rodents from three species and 35 rodents from five species of rodents were collected from Heilongjiang and Yunnan Provinces, respectively. Although the number and number of species of rodents trapped in the northeast were fewer than those in the southwest, viruses annotated from rodents in Heilongjiang were more diverse than those in Yunnan. Rodents carried 22 virus families in Heilongjiang and 13 families in Yunnan. Sequences assembled from Rattus norvegicus were annotated to the M, L, and S segments of HV, and all were clustered within the Seoul-type hantavirus (SEOV). There were 2 (R81Q, S698T) and 4 (K153R, M168I, I279S, and R1790K) amino acid site substitutions in M and L compared with the versions in the most homologous strains. Two BeiV isolates from Rattus norvegicus were closely related to BeiV from brown rats in Hong Kong, with high bootstrap values of >90% in the N segment and > 95% in the L segment. They were further clustered with Tailam virus, forming a distinct group in Paramyxoviridae.ConclusionThe rodents from Heilongjiang and Yunnan located in northeast and southwest China, respectively, had different viral spectra, and only one-third (10/32) of virus families were detected in both areas. The predominant viruses were HV and BeiV in the Hantaviridae and Paramyxoviridae families, respectively. Rodent-borne viruses in the same species were similar in different geographic disparate areas owing to their similar close contact with human habitats and human activities. Additional attention should be given to the monitoring of neglected rodent-borne viruses, especially opportunistic viruses with currently low loads. |
| first_indexed | 2024-12-24T00:00:09Z |
| format | Article |
| id | doaj.art-24d84a808ba24171b3b38be8ae253c06 |
| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-12-24T00:00:09Z |
| publishDate | 2022-02-01 |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-24d84a808ba24171b3b38be8ae253c062022-12-21T17:25:09ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-02-011210.3389/fmicb.2021.701089701089Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest ChinaTeng Zhao0Yun-qi Dang1Yun-qi Dang2Ao-nan Wang3Ao-nan Wang4He-ting Gao5Heng-duan Zhang6Dan Xing7Bo-qi Li8Bo-qi Li9Yong-jiu Li10Zhu Liu11Chun-xiao Li12State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, ChinaState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, ChinaCollege of Life Science and Technology, Mudanjiang Normal University, Heilongjiang, ChinaState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, ChinaCollege of Life Science and Technology, Mudanjiang Normal University, Heilongjiang, ChinaState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, ChinaState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, ChinaState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, ChinaState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, ChinaCollege of Life Science and Technology, Mudanjiang Normal University, Heilongjiang, ChinaRaohe Customs, Heilongjiang, ChinaCollege of Life Science and Technology, Mudanjiang Normal University, Heilongjiang, ChinaState Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, ChinaObjectiveWild animal pathogen surveillance will help to understand the next possible pandemic in advance. Rodents, which have close contact with humans, are generally regarded as a key factor for zoonotic disease control. Given the variation in rodent virus composition in diverse ecologies, we conducted a study on the viral infection of rodents of diverse species in different typical environments of Heilongjiang and Yunnan Provinces, located in northeastern and southwestern China, respectively.MethodsViral metagenomics sequencing and bioinformatic analysis were performed to determine the different distributions of rodent-borne viruses in typical environments of Heilongjiang and Yunnan Provinces, China. After viral culture and PCR confirmation, genomic and phylogenetic quantitative analysis was performed on the detected hantaviruses (HVs) and Beilong viruses (BeiVs).ResultsNineteen rodents from three species and 35 rodents from five species of rodents were collected from Heilongjiang and Yunnan Provinces, respectively. Although the number and number of species of rodents trapped in the northeast were fewer than those in the southwest, viruses annotated from rodents in Heilongjiang were more diverse than those in Yunnan. Rodents carried 22 virus families in Heilongjiang and 13 families in Yunnan. Sequences assembled from Rattus norvegicus were annotated to the M, L, and S segments of HV, and all were clustered within the Seoul-type hantavirus (SEOV). There were 2 (R81Q, S698T) and 4 (K153R, M168I, I279S, and R1790K) amino acid site substitutions in M and L compared with the versions in the most homologous strains. Two BeiV isolates from Rattus norvegicus were closely related to BeiV from brown rats in Hong Kong, with high bootstrap values of >90% in the N segment and > 95% in the L segment. They were further clustered with Tailam virus, forming a distinct group in Paramyxoviridae.ConclusionThe rodents from Heilongjiang and Yunnan located in northeast and southwest China, respectively, had different viral spectra, and only one-third (10/32) of virus families were detected in both areas. The predominant viruses were HV and BeiV in the Hantaviridae and Paramyxoviridae families, respectively. Rodent-borne viruses in the same species were similar in different geographic disparate areas owing to their similar close contact with human habitats and human activities. Additional attention should be given to the monitoring of neglected rodent-borne viruses, especially opportunistic viruses with currently low loads.https://www.frontiersin.org/articles/10.3389/fmicb.2021.701089/fullrodentsviral metagenomicshantavirusBeilong virusphylogenetics |
| spellingShingle | Teng Zhao Yun-qi Dang Yun-qi Dang Ao-nan Wang Ao-nan Wang He-ting Gao Heng-duan Zhang Dan Xing Bo-qi Li Bo-qi Li Yong-jiu Li Zhu Liu Chun-xiao Li Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China Frontiers in Microbiology rodents viral metagenomics hantavirus Beilong virus phylogenetics |
| title | Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China |
| title_full | Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China |
| title_fullStr | Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China |
| title_full_unstemmed | Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China |
| title_short | Viral Metagenomics Analysis of Rodents From Two Border Provinces Located in Northeast and Southwest China |
| title_sort | viral metagenomics analysis of rodents from two border provinces located in northeast and southwest china |
| topic | rodents viral metagenomics hantavirus Beilong virus phylogenetics |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.701089/full |
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