Isolation and molecular characterization of Chikungunya virus from the Andaman and Nicobar archipelago, India: evidence of an East, Central, and South African genotype

2011 ◽  
Vol 57 (12) ◽  
pp. 1073-1077 ◽  
Author(s):  
N. Muruganandam ◽  
I.K. Chaaithanya ◽  
G.S. Senthil ◽  
A.N. Shriram ◽  
D. Bhattacharya ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South African ◽  
Chikungunya Virus ◽  
Clinical Symptoms ◽  
East Central ◽  
Chikungunya Fever ◽  
The Family ◽  
First Time ◽  
Virus Isolates

Chikungunya virus (CHIKV) is an Alphavirus belonging to the family Togaviridae. In 2006, CHIKV infection struck the Andaman and Nicobar archipelago, with an attack rate of 60%. There were more than 10 cases with acute flaccid paralysis simulating the Guillian Barre Syndrome. The majority of the patients presented severe joint pain. The cause for such an explosive nature of the outbreak with increased morbidity was not known. The isolation of CHIKV was attempted and succeeded from nine subjects presenting clinical symptoms of Chikungunya fever. The cDNA of all the isolates was sequenced for partial E1 and nsP1 genes. Sequences were aligned based on the double locus sequence typing concept. The phylogenetic analysis shows that sequences of Andaman isolates grouped with the East, Central, and South African genotype of virus isolates from India, Sri Lanka, and Réunion. The genetic distance between Andaman isolates and the Réunion isolates was very small. The phylogenetic analysis confirmed the origin of the isolates responsible for the first ever confirmed CHIKV outbreak in these islands to be the East, Central, and South African genotype. In this manuscript, we discuss the involvement of the East, Central, and South African strain with the Chikungunya fever outbreak in this archipelago and double locus sequence typing as a first time approach.

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 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 Molecular Epidemiology, Evolution and Reemergence of Chikungunya Virus in South Asia

2021 ◽  
Vol 12 ◽  
Author(s):  
Nadim Sharif ◽  
Mithun Kumar Sarkar ◽  
Rabeya Nahar Ferdous ◽  
Shamsun Nahar Ahmed ◽  
Md. Baki Billah ◽  
...  
Keyword(s):  
South Asia ◽  
South African ◽  
Chikungunya Virus ◽  
Clinical Symptoms ◽  
Febrile Illness ◽  
Control Measures ◽  
Effective Control ◽  
East Central ◽  
Vector Mosquito ◽  
Central South

Chikungunya virus (CHIKV) is a vector (mosquito)-transmitted alphavirus (family Togaviridae). CHIKV can cause fever and febrile illness associated with severe arthralgia and rash. Genotypic and phylogenetic analysis are important to understand the spread of CHIKV during epidemics and the diversity of circulating strains for the prediction of effective control measures. Molecular epidemiologic analysis of CHIKV is necessary to understand the complex interaction of vectors, hosts and environment that influences the genotypic evolution of epidemic strains. In this study, different works published during 1950s to 2020 concerning CHIKV evolution, epidemiology, vectors, phylogeny, and clinical outcomes were analyzed. Outbreaks of CHIKV have been reported from Bangladesh, Bhutan, India, Pakistan, Sri Lanka, Nepal, and Maldives in South Asia during 2007–2020. Three lineages- Asian, East/Central/South African (ECSA), and Indian Ocean Lineage (IOL) are circulating in South Asia. Lineage, ECSA and IOL became predominant over Asian lineage in South Asian countries during 2011–2020 epidemics. Further, the mutant E1-A226V is circulating in abundance with Aedes albopictus in India, Bangladesh, Nepal, and Bhutan. CHIKV is underestimated as clinical symptoms of CHIKV infection merges with the symptoms of dengue fever in South Asia. Failure to inhibit vector mediated transmission and predict epidemics of CHIKV increase the risk of larger global epidemics in future. To understand geographical spread of CHIKV, most of the studies focused on CHIKV outbreak, biology, pathogenesis, infection, transmission, and treatment. This updated study will reveal the collective epidemiology, evolution and phylogenies of CHIKV, supporting the necessity to investigate the circulating strains and vectors in South Asia.

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 Detection of Chikungunya Virus Antigen by a Novel Rapid Immunochromatographic Test

2014 ◽  
Vol 53 (2) ◽  
pp. 382-388 ◽  
Author(s):  
Tamaki Okabayashi ◽  
Tadahiro Sasaki ◽  
Promsin Masrinoul ◽  
Nantarat Chantawat ◽  
Sutee Yoksan ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
South African ◽  
Diagnostic Test ◽  
Chikungunya Virus ◽  
Virus Antigen ◽  
Rt Pcr ◽  
Public Health Importance ◽  
East Central ◽  
Chikungunya Fever ◽  
Central South

Chikungunya fever is a mosquito-borne disease of key public health importance in tropical and subtropical countries. Although severe joint pain is the most distinguishing feature of chikungunya fever, diagnosis remains difficult because the symptoms of chikungunya fever are shared by many pathogens, including dengue fever. The present study aimed to develop a new immunochromatographic diagnosis test for the detection of chikungunya virus antigen in serum. Mice were immunized with isolates from patients with Thai chikungunya fever, East/Central/South African genotype, to produce mouse monoclonal antibodies against chikungunya virus. Using these monoclonal antibodies, a new diagnostic test was developed and evaluated for the detection of chikungunya virus. The newly developed diagnostic test reacted with not only the East/Central/South African genotype but also with the Asian and West African genotypes of chikungunya virus. Testing of sera from patients suspected to have chikungunya fever in Thailand (n= 50), Laos (n= 54), Indonesia (n= 2), and Senegal (n= 6) revealed sensitivity, specificity, and real-time PCR (RT-PCR) agreement values of 89.4%, 94.4%, and 91.1%, respectively. In our study using serial samples, a new diagnostic test showed high agreement with the RT-PCR within the first 5 days after onset. A rapid diagnostic test was developed using mouse monoclonal antibodies that react with chikungunya virus envelope proteins. The diagnostic accuracy of our test is clinically acceptable for chikungunya fever in the acute phase.

scholarly journals Following in the Footsteps of the Chikungunya Virus in Brazil: The First Autochthonous Cases in Amapá in 2014 and Its Emergence in Rio de Janeiro during 2016

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 623 ◽  
Author(s):  
Thiara de Souza ◽  
Edcelha Ribeiro ◽  
Valmir Corrêa ◽  
Paulo Damasco ◽  
Carla Santos ◽  
...  
Keyword(s):  
South African ◽  
Rio De Janeiro ◽  
Clinical Symptoms ◽  
Conjunctival Hyperemia ◽  
East Central ◽  
Lower Back ◽  
Two Samples ◽  
First Time ◽  
Central South ◽  
A226v Mutation

Currently, Brazil lives a triple arboviruses epidemic (DENV, ZIKV and CHIKV) making the differential diagnosis difficult for health professionals. Here, we aimed to investigate chikungunya cases and the possible occurrence of co-infections during the epidemic in Amapá (AP) that started in 2014 when the first autochthonous cases were reported and in Rio de Janeiro (RJ) in 2016. We further performed molecular characterization and genotyping of representative strains. In AP, 51.4% of the suspected cases were confirmed for CHIKV, 71.0% (76/107). Of those, 24 co-infections by CHIKV/DENV, two by CHIKV/DENV-1, and two by CHIKV/DENV-4 were observed. In RJ, 76.9% of the suspected cases were confirmed for CHIKV and co-infections by CHIKV/DENV (n = 8) and by CHIKV/ZIKV (n = 17) were observed. Overall, fever, arthralgia, myalgia, prostration, edema, exanthema, conjunctival hyperemia, lower back pain, dizziness, nausea, retroorbital pain, and anorexia were the predominating chikungunya clinical symptoms described. All strains analyzed from AP belonged to the Asian genotype and no amino acid changes were observed. In RJ, the East-Central-South-African genotype (ECSA) circulation was demonstrated and no E1-A226V mutation was observed. Despite this, an E1-V156A substitution was characterized in two samples and for the first time, the E1-K211T mutation was reported in all samples analyzed.

scholarly journals Complete Coding Sequences of 22 East/Central/South African Genotype Chikungunya Virus Isolates from Thailand (2018 to 2019)

2020 ◽  
Vol 9 (42) ◽  
Author(s):  
Piyawan Chinnawirotpisan ◽  
Sarunyou Chusri ◽  
Wudtichai Manasatienkij ◽  
Khajohn Joonlasak ◽  
Angkana T. Huang ◽  
...  
Keyword(s):  
South African ◽  
Chikungunya Virus ◽  
Viral Infectivity ◽  
Genome Sequences ◽  
East Central ◽  
Coding Sequences ◽  
Content Type ◽  
Central South ◽  
Virus Isolates ◽  
Virus Strains

ABSTRACT The coding-complete genome sequences of 22 chikungunya virus strains collected from the 2018–2019 outbreak in Thailand are reported. All sequences belong to the East/Central/South African (ECSA) genotype and contain two mutations, E1:K211E and E2:V264A, which were previously shown to be associated with increased viral infectivity, dissemination, and transmission in Aedes aegypti.

scholarly journals Emergence and persistence of the Chikungunya virus East-Central-South-African genotype in Northeast Brazil

2017 ◽  
Author(s):  
Antonio Charlys da Costa ◽  
Julien Thézé ◽  
Shirley Cavalcante Vasconcelos Komninakis ◽  
Rodrigo Lopes Sanz-Duro ◽  
Marta Rejane Lemos Felinto ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South African ◽  
Chikungunya Virus ◽  
Northeast Brazil ◽  
Molecular Surveillance ◽  
East Central ◽  
Northeast Region ◽  
Central South

SummaryWe investigate an outbreak of exanthematous illness in Maceió, Alagoas, using molecular surveillance. Of 273 samples, 76% tested RT-qPCR positive for Chikungunya virus. Phylogenetic analysis reveals that the outbreak was caused by the East-Central-South-African genotype, and that this lineage has likely persisted since mid-2014 in Northeast Brazil.Article summary lineTransmission of the Chikungunya virus East-Central-South-African genotype has been ongoing in the Northeast region of Brazil since mid-2014.

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