scholarly journals Source-tracking of the Chinese Chikungunya viruses suggests that Indian subcontinent and Southeast Asia act as major hubs for the recent global spread of Chikungunya virus

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Shaofu Qiu ◽  
Jinpeng Guo ◽  
Peihan Li ◽  
Peng Li ◽  
Xinying Du ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Southeast Asia ◽  
South African ◽  
Chikungunya Virus ◽  
Indian Subcontinent ◽  
Health Concern ◽  
Source Tracking ◽  
Global Spread ◽  
The Indian Ocean ◽  
Globally Distributed

Abstract Background Chikungunya fever, caused by the Chikungunya virus (CHIKV), has become a major global health concern, causing unexpected large outbreaks in Africa, Asia, Europe, and the Americas. CHIKV is not indigenous to China, and its origin in the country is poorly understood. In particular, there is limited understanding of the recent global spread of CHIKV in the context of the CHIKV epidemic. Methods Here we investigated a novel Chikungunya patient who came from Myanmar to China in August, 2019. Direct genome sequencing was performed via combined MinION sequencing and BGISEQ-500 sequencing. A complete CHIKV genome dataset, including 727 CHIKV genomes retrieved from GenBank and the genome sequenced in this study, was constructed. An updated and comprehensive phylogenetic analysis was conducted to understand the virus’s origin, evolution, transmission routes and genetic adaptation. Results All globally distributed CHIKV genomes were divided into West Africa, East/Central/South African and Asian genotypes. The genome sequenced in this study was located in the Indian Ocean lineage, and was closely related to a strain isolated from an Australian patient who returned from Bangladesh in 2017. A comprehensive phylogenetic analysis showed that the Chinese strains mainly originated from the Indian subcontinent and Southeast Asia. Further analyses indicated that the Indian subcontinent and Southeast Asia may act as major hubs for the recent global spread of CHIKV, leading to multiple outbreaks and epidemics. Moreover, we identified 179 distinct sites, including some undescribed sites in the structural and non-structural proteins, which exhibited apparent genetic variations associated with different CHIKV lineages. Conclusions Here we report a novel CHIKV isolate from a chikungunya patient who came from Myanmar to China in 2019, and summarize the source and evolution of Chinese CHIKV strains. Our present findings provide a better understanding of the recent global evolution of CHIKV, highlighting the urgent need for strengthened surveillance against viral diversity.

scholarly journals Source-tracking of the Chinese Chikungunya Viruses Suggests That Indian Subcontinent and Southeast Asia Act as Major Hubs for the Recent Global Spread of Chikungunya Virus

2021 ◽  
Author(s):  
Shaofu Qiu ◽  
Jinpeng Guo ◽  
Peihan Li ◽  
Peng Li ◽  
Xinying Du ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Southeast Asia ◽  
South African ◽  
Chikungunya Virus ◽  
Indian Subcontinent ◽  
Health Concern ◽  
Source Tracking ◽  
Global Spread ◽  
The Indian Ocean ◽  
Globally Distributed

Abstract BackgroundChikungunya fever caused by Chikungunya virus (CHIKV) has become a major global health concern, which has caused un­expected large outbreaks in Africa, Asia, Europe, and the Ameri­cas. China is a non-indigenous region of CHIKV, and the origin of the Chinese CHIKV strains is not well understood. Especially, there is limited understanding of the recent global spread of CHIKV in the context of recent worldwide epidemic of CHIKV.MethodsHere we investigated a novel Chikungunya patient imported from Myanmar into China in August, 2019. The genome was sequenced directly from the serum sample by combined MinION sequencing with BGISEQ-500 sequencing. We constructed a complete CHIKV genome dataset, including 727 CHIKV genomes retrieved from Genbank and the genome sequenced in this study, and conducted an updated and comprehensive phylogenetic analysis to understand the origin, evolution, transmission routes and genetic adaptation of the virus.ResultsAll of the globally distributed CHIKV genomes were divided into three genotypes, including West Africa (WA), East/Central/South African (ECSA) and Asian genotypes. The genome sequenced in this study was located in the Indian Ocean lineage (IOL), and closely related to a strain isolated from a patient in Australia who returned from Bangladesh in 2017. Comprehensive phylogenetic analysis showed that the Chinese strains were mainly sourced from Indian subcontinent and Southeast Asia. Further analyses indicated that Indian subcontinent and Southeast Asia may act as major hubs for the recent global spread of CHIKV, leading to widespread epidemics and even many large outbreaks. Moreover, we identified 179 distinct sites containing some undescribed sites in the sP and nsP proteins, showing obvious genetic varieties associated with different CHIKV lineages.ConclusionsHere we reported a novel CHIKV isolate from a Chikungunya patient imported from Myanmar into China in 2019, and summarized the source and evolution of Chinese CHIKV strains. The present findings provided better understanding of the recent global evolution of CHIKV, highlighting the urgent need for the strengthened surveillance including the viral diversity surveillance.

scholarly journals A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1319
Author(s):  
Juthamas Phadungsombat ◽  
Hisham Imad ◽  
Mizanur Rahman ◽  
Emi E. Nakayama ◽  
Sajikapon Kludkleeb ◽  
...  
Keyword(s):  
Indian Ocean ◽  
Southeast Asia ◽  
South African ◽  
Chikungunya Virus ◽  
Indian Subcontinent ◽  
East Central ◽  
The Past ◽  
Clock Analysis ◽  
Central South ◽  
Molecular Clock Analysis

In recent decades, chikungunya virus (CHIKV) has become geographically widespread. In 2004, the CHIKV East/Central/South African (ECSA) genotype moved from Africa to Indian ocean islands and India followed by a large epidemic in Southeast Asia. In 2013, the CHIKV Asian genotype drove an outbreak in the Americas. Since 2016, CHIKV has re-emerged in the Indian subcontinent and Southeast Asia. In the present study, CHIKVs were obtained from Bangladesh in 2017 and Thailand in 2019, and their nearly full genomes were sequenced. Phylogenetic analysis revealed that the recent CHIKVs were of Indian Ocean Lineage (IOL) of genotype ECSA, similar to the previous outbreak. However, these CHIKVs were all clustered into a new distinct sub-lineage apart from the past IOL CHIKVs, and they lacked an alanine-to-valine substitution at position 226 of the E1 envelope glycoprotein, which enhances CHIKV replication in Aedes albopictus. Instead, all the re-emerged CHIKVs possessed mutations of lysine-to-glutamic acid at position 211 of E1 and valine-to-alanine at position 264 of E2. Molecular clock analysis suggested that the new sub-lineage CHIKV was introduced to Bangladesh around late 2015 and Thailand in early 2017. These results suggest that re-emerged CHIKVs have acquired different adaptations than the previous CHIKVs.

scholarly journals Complete Coding Sequence of a Case of Chikungunya Virus Imported into Australia

2017 ◽  
Vol 5 (19) ◽  
Author(s):  
Bixing Huang ◽  
Alyssa T. Pyke ◽  
Jamie McMahon ◽  
David Warrilow
Keyword(s):  
Phylogenetic Analysis ◽  
Virus Infection ◽  
Real Time ◽  
South African ◽  
Genome Sequencing ◽  
Reverse Transcription ◽  
Chikungunya Virus ◽  
East Central ◽  
Reverse Transcription Pcr ◽  
Central South

ABSTRACT A case of chikungunya virus infection was imported from India into Australia in late 2016. Infection was diagnosed by real-time reverse transcription-PCR and confirmed by culture isolation and genome sequencing. Phylogenetic analysis of the genome sequence indicated that the virus grouped with the east/central/south African genotype.

scholarly journals Complete Coding Sequence of a Chikungunya Virus Strain Imported into Slovenia from Thailand in Late 2018

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Samo Zakotnik ◽  
Misa Korva ◽  
Nataša Knap ◽  
Barbara Robnik ◽  
Nina Gorišek Miksić ◽  
...  
Keyword(s):  
Cell Culture ◽  
Phylogenetic Analysis ◽  
Envelope Protein ◽  
Viral Genome ◽  
Chikungunya Virus ◽  
Whole Genome ◽  
Reverse Transcription Pcr ◽  
The Indian Ocean ◽  
Complete Viral Genome ◽  
A226v Mutation

A case of chikungunya virus infection was imported from Thailand into Slovenia in late 2018. The infection was diagnosed using real-time reverse transcription-PCR, the virus was isolated in cell culture, and the whole genome was sequenced. Phylogenetic analysis of the nearly complete viral genome indicated that the virus belongs to the Indian Ocean lineage but does not possess the A226V mutation in the envelope protein E1.

scholarly journals Detection of East/Central/South African genotype Chikungunya virus during an outbreak in a southeastern state of Brazil

2018 ◽  
Vol 146 (16) ◽  
pp. 2056-2058 ◽  
Author(s):  
C. Lessa-Aquino ◽  
K. S. Trinta ◽  
C. P. Pestana ◽  
M. O. Ribeiro ◽  
M. V. F. Sucupira ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South African ◽  
Acute Phase ◽  
Chikungunya Virus ◽  
Febrile Illness ◽  
Partial Sequence ◽  
East Central ◽  
Qrt Pcr ◽  
Central South ◽  
Sera Samples

AbstractChikungunya virus (CHIKV) is an arbovirus transmitted by Aedes mosquitoes that was first identified in Brazil in 2014. It causes a febrile illness characterised by severe arthralgia and rash. Our group investigated a suspected CHIKV outbreak in Governador Valadares, state of Minas Gerais, Brazil and from 25 acute-phase patients, 10 had qRT-PCR positive sera samples and had E1 partial sequence amplified and Sanger sequenced. Samples were identified as East/Central/South African (ECSA) genotype by phylogenetic analysis and clustered with CHIKV sequences isolated in the neighbour state of Bahia. Our findings confirm previous predictions that ECSA genotype would spread through northeast and southeast of Brazil.

Chikungunya outbreak in Karachi Pakistan 2016-2017: an analysis of viral isolates

2020 ◽  
pp. 1-11
Author(s):  
Dhani Prakoso ◽  
Kelli Barr ◽  
Kehkashan Imtiaz ◽  
Joveria Farooqi ◽  
Erum Khan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South African ◽  
Chikungunya Virus ◽  
Amino Acid Change ◽  
Nucleotide Substitution ◽  
Febrile Illness ◽  
East Central ◽  
E1 Protein ◽  
Central South ◽  
Viral Isolates

Abstract In December 2016 physicians in Karachi, Pakistan,witnessed an increase in patients presenting with febrile illness and severe polyarthralgia. Subsequently, chikungunya virus(CHIKV) was isolated from three patients. This virus was sequenced and compared with other isolates of CHIKVobtained in India and Pakistan during recent outbreaks. Phylogenetic analysis indicated that the Karachi isolates were most similar to the East Central South African CHIKV lineage and showed sequence homology to isolates obtained in other parts of Pakistan and India. More importantly, two of the CHIKV isolates had a nucleotide substitution in the E1 gene corresponding to an amino acid change at chain F portion of the E1 protein. Continuous...

scholarly journals Molecular Characterization of Chikungunya Virus Isolates From Two Localized Outbreaks During 2014-2019 in Kerala, India

2021 ◽  
Author(s):  
Anukumar Balakrishnan ◽  
Asia Devi Thounaojam ◽  
Aishwarya Babu ◽  
Jijo Koshy ◽  
Nikhil T L ◽  
...  
Keyword(s):  
South African ◽  
Chikungunya Virus ◽  
Novel Mutation ◽  
Indian Subcontinent ◽  
Virus Transmission ◽  
Amino Acid Position ◽  
East Central ◽  
Sequencing Studies ◽  
Central South

Abstract After the 2005-2009 chikungunya epidemic, intermittent outbreaks were reported in many parts of India. The outbreaks were caused by either locally circulating strains or imported viruses. Virus transmission route can be traced by complete genome sequencing studies. We investigated two outbreaks in the year 2014 and 2019 in Kerala, India. The chikungunya virus (CHIKV) was isolated from the samples and whole genome was sequenced for a 2014 isolate and a 2019 isolate. The phylogenetic tree revealed that the isolates formed a separate group with 2019 isolate from Pune, Maharashtra and belonged to the East/ Central/ South African (ECSA) genotype, Indian subcontinent sub lineage of Indian Ocean Lineage (IOL). A novel mutation at amino acid position 76 of E2 gene was observed in the group. The phylogenetic results suggest that the outbreaks might have caused by a virus, which has been circulating in India since 2014. Furthermore a detailed study is necessary to find out the evolution of CHIKV in India.

scholarly journals First report of the East-Central South African Genotype of Chikungunya Virus in Rio de Janeiro, Brazil

2016 ◽  
Author(s):  
Thiara Manuele Alves de Souza ◽  
Elzinandes Leal de Azeredo ◽  
Jéssica Badolato Corrêa da Silva ◽  
Paulo Vieira Damasco ◽  
Carla Cunha Santos ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South African ◽  
Molecular Characterization ◽  
Rio De Janeiro ◽  
Chikungunya Virus ◽  
Febrile Illness ◽  
East Central ◽  
The North ◽  
Igm Elisa ◽  
Central South

AbstractBackgroundChikungunya virus (CHIKV) is an arbovirus that causes an acute febrile illness characterized by severe and debilitating arthralgia. In Brazil, the Asian and East-Central South African (ECSA) genotypes are circulating in the north and northeast of the country, respectively. In 2015, the first autochthonous cases in Rio de Janeiro, Brazil were reported but until now the circulating strains have not been characterized. Therefore, we aimed here to perform the molecular characterization and phylogenetic analysis of CHIKV strains circulating in the 2016 outbreak occurred in the municipality of Rio de Janeiro.MethodsThe cases analyzed in this study were collected at a private Hospital, from April 2016 to May 2016, during the chikungunya outbreak in Rio de Janeiro, Brazil. All cases were submitted to the Real Time RT-PCR for CHIKV genome detection and to anti-CHIKV IgM ELISA. Chikungunya infection was laboratorially confirmed by at least one diagnostic method and, randomly selected positive cases (n=10), were partially sequenced (CHIKV E1 gene) and analyzed.ResultsThe results showed that all the samples grouped in ECSA genotype branch and the molecular characterization of the fragment did not reveal the A226V mutation in the Rio de Janeiro strains analyzed, but a K211T amino acid substitution was observed for the first time in all samples and a V156A substitution in two of ten samples.ConclusionsPhylogenetic analysis and molecular characterization reveals the circulation of the ECSA genotype of CHIKV in the city of Rio de Janeiro, Brazil and two amino acids substitutions (K211T and V156A) exclusive to the CHIKV strains obtained during the 2016 epidemic, were reported.

scholarly journals Northward movement of East Central South African genotype of Chikungunya virus causing an epidemic between 2006-2010 in India

2012 ◽  
Vol 6 (07) ◽  
pp. 563-571 ◽  
Author(s):  
Priyanka Singh ◽  
Veena Mittal ◽  
Moshahid A Rizvi ◽  
Dipesh Bhattacharya ◽  
Mala Chhabra ◽  
...  
Keyword(s):  
South African ◽  
Chikungunya Virus ◽  
South India ◽  
Indian Subcontinent ◽  
Virus Transmission ◽  
Central India ◽  
Nucleotide Sequencing ◽  
East Central ◽  
Northern India ◽  
Central South

Introduction: Re-emergence of chikungunya virus in South India after a gap of 32 years in 2006 affected over a million people in the Indian subcontinent. We kept a close vigil over the emerging trend of this virus between 2006-2010 with a view to establish the identity of the circulating genotype(s) and to determine the route of virus transmission in different parts of India. Methodology: Nucleotide sequencing of the E1 gene region from 36 strains of chikungunya virus from three states in northern India was performed for this present study. Forty-four previously reported E1 sequences, retrieved from the global genome data base were used for making a phylogenetic tree. Results: BLAST search revealed 99% homology of the northern Indian strains of the 2006-2010 outbreak with the Reunion Island isolates of 2006. Northern Indian strains of this study clustered with the East Central South African (ECSA) genotype. Conclusions: Findings indicate that the currently circulating strain of chikungunya virus in northern India had its origin from the 2006 epidemic strain of South India that moved toward northern India via the western central India between 2006-2010 in a phased manner with dominance of the ECSA genotype and not the Asian genotype.

scholarly journals Chikungunya virus infection: molecular biology, clinical characteristics, and epidemiology in Asian countries

2021 ◽  
Vol 28 (1) ◽  
Author(s):  
Sarawut Khongwichit ◽  
Jira Chansaenroj ◽  
Chintana Chirathaworn ◽  
Yong Poovorawan
Keyword(s):  
Indian Ocean ◽  
Southeast Asia ◽  
Chikungunya Virus ◽  
Health Concern ◽  
Adaptive Mutation ◽  
Genotype Distribution ◽  
Asian Countries ◽  
Disease Manifestation ◽  
Southwest Indian Ocean ◽  
South And Southeast Asia

AbstractChikungunya virus (CHIKV) is a re-emerging mosquito-borne human pathogen that causes chikungunya fever, which is typically accompanied by severe joint pain. In Asia, serological evidence indicated that CHIKV first emerged in 1954. From the 1950’s to 2005, sporadic CHIKV infections were attributed to the Asian genotype. However, the massive outbreak of CHIKV in India and the Southwest Indian Ocean Islands in 2005 has since raised chikungunya as a worldwide public health concern. The virus is spreading globally, but mostly in tropical and subtropical regions, particularly in South and Southeast Asia. The emergence of the CHIKV East/Central/South African genotype-Indian Ocean lineage (ECSA-IOL) has caused large outbreaks in South and Southeast Asia affected more than a million people over a decade. Notably, the massive CHIKV outbreaks before 2016 and the more recent outbreak in Asia were driven by distinct ECSA lineages. The first significant CHIKV ECSA strains harbored the Aedes albopictus-adaptive mutation E1: A226V. More recently, another mass CHIKV ECSA outbreak in Asia started in India and spread beyond South and Southeast Asia to Kenya and Italy. This virus lacked the E1: A226V mutation but instead harbored two novel mutations (E1: K211E and E2: V264A) in an E1: 226A background, which enhanced its fitness in Aedes aegypti. The emergence of a novel ECSA strain may lead to a more widespread geographical distribution of CHIKV in the future. This review summarizes the current CHIKV situation in Asian countries and provides a general overview of the molecular virology, disease manifestation, diagnosis, prevalence, genotype distribution, evolutionary relationships, and epidemiology of CHIKV infection in Asian countries over the past 65 years. This knowledge is essential in guiding the epidemiological study, control, prevention of future CHIKV outbreaks, and the development of new vaccines and antivirals targeting CHIKV.

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