1
|
Wu X, Liu G, Chang Y, Zheng M, Liu L, Xia X, Feng Y. Rapid and sensitive detection of chikungunya virus using one-tube, reverse transcription, semi-nested multi-enzyme isothermal rapid amplification, and lateral flow dipstick assays. J Clin Microbiol 2024; 62:e0038324. [PMID: 39140738 PMCID: PMC11389142 DOI: 10.1128/jcm.00383-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024] Open
Abstract
Chikungunya fever is an acute infectious disease caused by chikungunya virus (CHIKV), which is transmitted by Aedes mosquitoes. Simple, rapid, and sensitive detection of CHIKV is critical for its prevention and spread. To address this issue, we combined one-tube, reverse transcription semi-nested, multi-enzyme isothermal rapid amplification, and lateral flow dipstick strips assay to detect CHIKV RNA. The study used a 318-bp gene fragment of CHIKV NSP4 as the target of the assay. This method of amplification takes 30 min for two-step amplification at 39°C. The dilution of amplification products was added to the LFD strip with results visible to the naked eye after 10 min. The method has a sensitivity of 1 copy/μL for the detection of CHIKV RNA, which is 100-fold higher than the conventional reverse transcription-multi-enzyme isothermal rapid amplification and 10-fold higher than the reverse transcription quantitative PCR (RT-qPCR) method. In addition, the method demonstrated good specificity and a better detection rate (85.7%, 18 of 21) than RT-qPCR (80.9%, 17 of 21) in clinically confirmed patient plasma samples. Thus, the rapid CHIKV RNA assay developed in this study will be an important tool for the rapid and accurate screening of patients for chikungunya fever. IMPORTANCE This study presents a new one-tube, reverse transcription semi-nested, multi-enzyme isothermal rapid amplification assay combined with lateral flow dipstick strips for the detection of CHIKV. This technique significantly improves sensitivity and outperforms RT-qPCR for the detection of CHIKV, especially in samples with low viral loads. It is also significantly faster than conventional RT-qPCR and does not require special equipment or a standard PCR laboratory. The combination of the isothermal amplification technology developed in this study with point-of-care molecular testing offers the potential for rapid, on-site, low-cost molecular diagnosis of CHIKV.
Collapse
Affiliation(s)
- Xinlin Wu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Yunnan Kecan Biotechnology Co., Ltd, Kunming, Yunnan, China
| | - Gaowen Liu
- Yunnan Kecan Biotechnology Co., Ltd, Kunming, Yunnan, China
| | - Yingchao Chang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Yunnan Kecan Biotechnology Co., Ltd, Kunming, Yunnan, China
| | - Mengyuan Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Yunnan Kecan Biotechnology Co., Ltd, Kunming, Yunnan, China
| | - Xueshan Xia
- Yunnan Provincial Key Laboratory of Public Health and Biosafety, Kunming Medical University, Kunming, Yunnan, China
| | - Yue Feng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Public Health and Biosafety, Kunming Medical University, Kunming, Yunnan, China
| |
Collapse
|
2
|
Chantasrisawad N, Boonyasuppayakorn S, Anugulruengkitt S, Puthanakit T. CHARACTERIZATION OF CLINICAL AND BIOLOGIC MANIFESTATIONS OF CHIKUNGUNYA AMONG CHILDREN IN AN URBAN AREA, THAILAND: A RETROSPECTIVE COHORT STUDY. Pediatr Infect Dis J 2024:00006454-990000000-00990. [PMID: 39230282 DOI: 10.1097/inf.0000000000004542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Chikungunya virus (CHIKV), transmitted by Aedes mosquitoes, has reemerged in Southeast Asia since 2019. A retrospective review of CHIKV cases was conducted. Children commonly presented with high-grade fever, rash, arthralgia, and lymphopenia. Neurological manifestations or shock occurred in 20% of hospitalized children. These findings indicate the need for increased vigilance for CHIKV alongside dengue in travelers from Southeast Asia with suspected mosquito-borne viral infections.
Collapse
Affiliation(s)
- Napaporn Chantasrisawad
- From the Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital The Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence for Pediatric Infectious Diseases and Vaccines
- Department of Pediatrics
| | - Siwaporn Boonyasuppayakorn
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Thanyawee Puthanakit
- Center of Excellence for Pediatric Infectious Diseases and Vaccines
- Department of Pediatrics
| |
Collapse
|
3
|
Su L, Lou X, Yan H, Yang Z, Mao H, Yao W, Sun Y, Pan J, Zhang Y. Importation of a novel Indian Ocean lineage carrying E1-K211E and E2-V264A of Chikungunya Virus in Zhejiang Province, China, in 2019. Virus Genes 2023; 59:693-702. [PMID: 37468826 PMCID: PMC10499945 DOI: 10.1007/s11262-023-02020-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023]
Abstract
The chikungunya virus (CHIKV) is widespread. In Zhejiang province, China, CHIKV infection is often associated with travelers from tropical and subtropical countries. In the present study, three CHIKV isolates from serum samples of travelers in Zhejiang province in 2019 were sequenced, and phylogenetically analyzed to study their molecular characteristics. Sequence analysis showed that the non-structural protein and the structural protein had 37 and 28 amino acid mutations, respectively; no mutation site was found at the E1-A226 residue, which could increase the adaptability of CHIKV to Aedes albopictus. All three samples carried two mutations, namely, E1-K211E and E2-V264A, which were introduced to Bangladesh around late 2015 and Thailand in early 2017. Phylogenetic analysis revealed that these three CHIKVs were Indian Ocean lineage of the East Africa/Central/South Africa genotype (ECSA) and that the MF773566 strain from Bangladesh (Australia/Bangladesh 2017) had the closest evolutionary relationship. The three CHICKs imported into Zhejiang province in 2019 belonged to the ECSA genotype and had multiple amino acid variation sites. The variation in the three samples provides a certain reference for the subsequent research on CHIKV evolution.
Collapse
Affiliation(s)
- Lingxuan Su
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| | - Xiuyu Lou
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| | - Hao Yan
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| | - Zhangnv Yang
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| | - Haiyan Mao
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| | - Wenwu Yao
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| | - Yi Sun
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| | - Junhang Pan
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| | - Yanjun Zhang
- Zhejiang Provincial Center of Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051 China
| |
Collapse
|
4
|
Wang F, Zhu Y, Zhang H, Fan J, Leng P, Zhou J, Yao S, Yang D, Liu Y, Wang J, Yao J, Zhou Y, Zhao T. Spatial and temporal analyses of the influences of meteorological and environmental factors on Aedes albopictus (Diptera: Culicidae) population dynamics during the peak abundance period at a city scale. Acta Trop 2023:106964. [PMID: 37307888 DOI: 10.1016/j.actatropica.2023.106964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
Aedes albopictus (Diptera: Culicidae) is a major vector of multiple diseases. While vaccines have been developed, preventing these Aedes-borne diseases continues to primarily depend on monitoring and controlling the vector population. Despite increasing research on the impacts of various factors on Ae. albopictus population dynamics, there is still no consensus on how meteorological or environmental factors affect vector distribution. In this study, the relationships between mosquito abundance and meteorological and environmental indicators were examined at the town level based on data collected from July to September, the peak abundance period of 2019 in Shanghai. In addition to performing Poisson regression, we employed the geographically weighted Poisson regression model to account for spatial dependency and heterogeneity. The result showed that the environmental factors (notably human population density, the Normalized Difference Vegetation Index (NDVI), socioeconomic deprivation, and road density) had more significant impacts than the meteorological variables in accounting for the spatial variation of mosquito abundance at a city scale. The dominant environmental variable differed in urban and rural places. Furthermore, our findings indicated that deprived townships are more susceptible to higher vector densities compared to non-deprived townships. Therefore, it is crucial not only to allocate more resources but also to increase attention towards controlling the vectors responsible for their transmission in these townships.
Collapse
Affiliation(s)
- Fei Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; Hongkou District Center for Disease Control and Prevention, Shanghai 200082, China
| | - Yiyi Zhu
- Department of Infectious Disease Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Hengduan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Junhua Fan
- Department of Infectious Disease Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Peien Leng
- Department of Infectious Disease Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Ji Zhou
- Shanghai Key Laboratory of Meteorology and Health, Shanghai Meteorological Bureau, Shanghai, 200030, China
| | - Shenjun Yao
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Dandan Yang
- Shanghai Key Laboratory of Meteorology and Health, Shanghai Meteorological Bureau, Shanghai, 200030, China
| | - Yao Liu
- Department of Infectious Disease Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Jingjing Wang
- Department of Infectious Disease Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Juanyi Yao
- Department of Infectious Disease Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Yibin Zhou
- Minhang District Center for Disease Control and Prevention, Shanghai 201011, China.
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.
| |
Collapse
|
5
|
Zou M, Su C, Li T, Zhang J, Li D, Luan N, Ma D, Liu J, Sun Q, Peng X, Liu H. Genetic Characterization of Chikungunya Virus Among Febrile Dengue Fever–Like Patients in Xishuangbanna, Southwestern Part of China. Front Cell Infect Microbiol 2022; 12:914289. [PMID: 35832380 PMCID: PMC9271616 DOI: 10.3389/fcimb.2022.914289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Co-infection of chikungunya virus (CHIKV) has been recently reported during dengue fever epidemics. However, the infection of CHIKV is often neglected due to its misdiagnosis as dengue virus (DENV) infection. In the summer of 2019 when dengue fever was epidemic, we collected 697 serum samples from febrile dengue fever–like patients in Xishuangbanna, southwestern part of China. DENV RNA was detectable in 99.42% of these patients. Notably, 88 patients (12.62%) showed the presence of CHIKV RNA, among which 86 patients were co-infected with DENV and CHIKV. We sequenced and analyzed the full genome of CHIKV virus in four out of 88 samples (two CHIKV infected and two co-infected). The results suggested that the four strains were all Asian genotype and had the highest homology (99.4%) with the SZ1239 strain (accession number MG664851) isolated in 2012 and possibly introduced from Indonesia. Further comparison with the conserved sequences in the whole genome of 47 strains of CHIKV showed that there were 13 and 15 amino acid mutants in structural proteins and non-structural proteins, respectively. The previously reported adaptive mutations of E2-W64R, E2-I211T, E2-K233E, E1-A98T, and E1-K211E occurred in the four strains of this study. In conclusion, this study reports a co-infection of CHIKV during the DENV epidemic in the city Xishuangbanna, 2019. Molecular epidemiology revealed that CHIKV identified in this study was indigenous and belongs to Asian lineage with lineage-specific mutations and some reported adaptive mutations, which is distinct from the recently reported CHIKV (East/Central/South African) in Ruili, the city next to Xishuangbanna.
Collapse
Affiliation(s)
- Meng Zou
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Chunyan Su
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Tingting Li
- Joint Laboratory for Prevention and Control of Cross-border Transmission Disease, People’s Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, China
| | - Jing Zhang
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Daiying Li
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Ning Luan
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Dehong Ma
- Joint Laboratory for Prevention and Control of Cross-border Transmission Disease, People’s Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, China
| | - Jiansheng Liu
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Hongqi Liu
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
- *Correspondence: Hongqi Liu,
| |
Collapse
|
6
|
Wang T, Fan ZW, Ji Y, Chen JJ, Zhao GP, Zhang WH, Zhang HY, Jiang BG, Xu Q, Lv CL, Zhang XA, Li H, Yang Y, Fang LQ, Liu W. Mapping the Distributions of Mosquitoes and Mosquito-Borne Arboviruses in China. Viruses 2022; 14:v14040691. [PMID: 35458421 PMCID: PMC9031751 DOI: 10.3390/v14040691] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/11/2022] [Accepted: 03/24/2022] [Indexed: 12/20/2022] Open
Abstract
The geographic expansion of mosquitos is associated with a rising frequency of outbreaks of mosquito-borne diseases (MBD) worldwide. We collected occurrence locations and times of mosquito species, mosquito-borne arboviruses, and MBDs in the mainland of China in 1954−2020. We mapped the spatial distributions of mosquitoes and arboviruses at the county level, and we used machine learning algorithms to assess contributions of ecoclimatic, socioenvironmental, and biological factors to the spatial distributions of 26 predominant mosquito species and two MBDs associated with high disease burden. Altogether, 339 mosquito species and 35 arboviruses were mapped at the county level. Culex tritaeniorhynchus is found to harbor the highest variety of arboviruses (19 species), followed by Anopheles sinensis (11) and Culex pipiens quinquefasciatus (9). Temperature seasonality, annual precipitation, and mammalian richness were the three most important contributors to the spatial distributions of most of the 26 predominant mosquito species. The model-predicted suitable habitats are 60–664% larger in size than what have been observed, indicating the possibility of severe under-detection. The spatial distribution of major mosquito species in China is likely to be under-estimated by current field observations. More active surveillance is needed to investigate the mosquito species in specific areas where investigation is missing but model-predicted probability is high.
Collapse
Affiliation(s)
- Tao Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Zheng-Wei Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Yang Ji
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Jin-Jin Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Guo-Ping Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Wen-Hui Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Hai-Yang Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Bao-Gui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Qiang Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Chen-Long Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Xiao-Ai Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
| | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
- Correspondence: (H.L.); (Y.Y.); (L.-Q.F.); (W.L.)
| | - Yang Yang
- College of Public Health and Health Professions and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
- Correspondence: (H.L.); (Y.Y.); (L.-Q.F.); (W.L.)
| | - Li-Qun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
- Correspondence: (H.L.); (Y.Y.); (L.-Q.F.); (W.L.)
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; (T.W.); (Z.-W.F.); (Y.J.); (J.-J.C.); (G.-P.Z.); (W.-H.Z.); (H.-Y.Z.); (B.-G.J.); (Q.X.); (C.-L.L.); (X.-A.Z.)
- Correspondence: (H.L.); (Y.Y.); (L.-Q.F.); (W.L.)
| |
Collapse
|
7
|
Phadungsombat J, Imad HA, Nakayama EE, Leaungwutiwong P, Ramasoota P, Nguitragool W, Matsee W, Piyaphanee W, Shioda T. Spread of a Novel Indian Ocean Lineage Carrying E1-K211E/E2-V264A of Chikungunya Virus East/Central/South African Genotype across the Indian Subcontinent, Southeast Asia, and Eastern Africa. Microorganisms 2022; 10:354. [PMID: 35208808 PMCID: PMC8878743 DOI: 10.3390/microorganisms10020354] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 01/27/2023] Open
Abstract
The Indian Ocean Lineage (IOL) of the chikungunya virus (CHIKV) East/Central/South African (ECSA) genotype, which originated in Kenya, spread to the Indian ocean and the Indian subcontinent, and then expanded through Southeast Asia in the previous decade. It carried an adaptive mutation E1-A226V, which enhances CHIKV replication in Aedes albopictus. However, the IOL CHIKV of the most recent outbreaks during 2016-2020 in India, Pakistan, Bangladesh, the Maldives, Myanmar, Thailand, and Kenya lacked E1-A226V but carried E1-K211E and E2-V264A. Recent CHIKV genome sequences of the Maldives and Thailand were determined, and their phylogenetic relationships were further investigated together with IOL sequences reported in 2004-2020 in the database. The results showed that the ancestral IOLs diverged to a sub-lineage E1-K211E/E2-V264A, probably in India around 2008, and caused sporadic outbreaks in India during 2010-2015 and in Kenya in 2016. The massive expansion of this new sub-lineage occurred after the acquisition of E1-I317V in other neighboring and remote regions in 2014-2020. Additionally, the phylogenetic tree indicated that independent clades formed according to the geographical regions and introduction timing. The present results using all available partial or full sequences of the recent CHIKVs emphasized the dynamics of the IOL sub-lineages in the Indian subcontinent, Southeast Asia, and Eastern Africa.
Collapse
Affiliation(s)
- Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
- Center for Infectious Disease Education and Research, Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan; (H.A.I.); (E.E.N.)
| | - Hisham A. Imad
- Center for Infectious Disease Education and Research, Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan; (H.A.I.); (E.E.N.)
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Emi E. Nakayama
- Center for Infectious Disease Education and Research, Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan; (H.A.I.); (E.E.N.)
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Pongrama Ramasoota
- Center of Excellence for Antibody Research (CEAR), Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Wang Nguitragool
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Wasin Matsee
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (W.M.); (W.P.)
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Watcharapong Piyaphanee
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (W.M.); (W.P.)
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Tatsuo Shioda
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
- Center for Infectious Disease Education and Research, Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan; (H.A.I.); (E.E.N.)
| |
Collapse
|