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 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.

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 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 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.

Molecular characterization and phylogenetic analysis of Chikungunya virus during the 2016 outbreak in Sergipe, northeastern Brazil

2020 ◽  
Author(s):  
Myrela C S Jesus ◽  
Rynat D O Chagas ◽  
Cliomar A Santos ◽  
Rafaela W F Santos ◽  
Gerlane S Barros ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South African ◽  
Molecular Characterization ◽  
Point Mutations ◽  
Northeastern Brazil ◽  
High Morbidity ◽  
East Central ◽  
E1 Protein ◽  
Rapid Spread ◽  
Central South

Abstract Background Chikungunya (CHIKV) is an arbovirus transmitted mainly by Aedes aegypti females. CHIKV has been highlighted as the pathogen with the greatest impact due to the high morbidity caused by the infection. In 2016, Brazil experienced an outbreak that affected almost 272 000 people. Here, we performed a molecular characterization and phylogenetic analysis of the CHIKV circulating in 2016 in the state of Sergipe, Brazil. Methods A partial region of the E1 gene of 16 CHIKV-positive samples from Sergipe State was amplified and sequenced. Results All sequences belonged to the East-Central-South-African genotype and three point mutations were verified. Two of them were silent mutations and one was a non-synonymous mutation, which changed lysine to threonine at position 211 in the E1 protein. This mutation was present in 81.2% of the sequences, as well as in other five Brazilian sequences from previous studies. This study found that CHIKV strains circulating in Sergipe during the 2016 outbreak belonged to two different haplotypes. Conclusions The strains circulating in Sergipe are phylogenetically close to other Brazilian samples circulating in the northeast and southeast of the country, as well as viruses circulating during the same period in Haiti, indicating the rapid spread of these haplotypes.

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.

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 Spread, circulation and predominance of chikungunya virus East/Central/South African genotype in Northeast and Southeast Brazil

2018 ◽  
Author(s):  
André R R Freitas ◽  
Robert Paulino-Ramírez ◽  
Rodrigo N Angerami ◽  
Pedro Mª Alarcón-Elbal
Keyword(s):  
South African ◽  
Chikungunya Virus ◽  
Vector Competence ◽  
Temperate Climate ◽  
Southeastern Brazil ◽  
East Central ◽  
Diapausing Eggs ◽  
Cold Tolerant ◽  
Asian Lineage ◽  
Central South

Two recent researches described the spread of East/Central/South African (ECSA) lineage of chikungunya virus (CHIKV) in the Northeastern and Southeastern Brazil (Charlys da Costa et al. 2017, Cunha et al. 2017) . Initial studies in Northern Brazil, as observed in Caribbean, identified the Asian as the circulating lineage of the chikungunya. However, da Charlys da Costa et al. and Cunha et al. reported the exclusive occurrence of ECSA in two different Brazilian regions: Northeast as well as in Rio de Janeiro State (Charlys da Costa et al. 2017, Cunha et al. 2017) , suggesting that the ECSA is the predominant lineage in highly populated Brazilian areas. Despite the well-described vector competence of Aedes mosquitoes for CHIKV transmission, Aedes(Stegomyia)albopictus seems to have a greater competence for transmission of ECSA lineage compared to the Asian lineage (Vega-Rúa et al. 2015) , particularly when variable temperatures mimicking daily fluctuations of temperate climate (Vega-Rúa et al. 2015) . This statement is consistent with the fact that A albopictus has not been denounced as a vector of large outbreaks of chikungunya caused by the Asian genotype. This invasive species have capability of cold-tolerant diapausing eggs, it is paramount to establishment in temperate areas (Mitchell 1995) and new regions are invaded each year (Kraemer et al. 2015) . The predominance of the ECSA lineage in Brazil represents a potential risk of CHIKV dispersion to areas where Ae. albopictus has a broader distribution, particularly in temperate climates, including United States and Europe (Kraemer et al. 2015) , territories with intense commercial and touristic relationship with Brazil. Furthermore, the predominance of ECSA in Brazil can contributes to a better comprehension of the current distinct epidemiological scenarios between Caribbean - where explosive epidemics occurred with Aedes(Stegomyia) aegypti and Asian lineage predominated - and Brazil - with an apparent slower dispersion of CHIKV, where Ae.aegypti predominate but ECSA was prevalent linage. Both studies highlighted the importance of virological surveillance for analysis of current epidemiological scenarios and prediction of potential patterns of spreading of arboviral diseases, locally and worldwide.

scholarly journals Spread, circulation and predominance of chikungunya virus East/Central/South African genotype in Northeast and Southeast Brazil

2018 ◽  
Author(s):  
André R R Freitas ◽  
Robert Paulino-Ramírez ◽  
Rodrigo N Angerami ◽  
Pedro Mª Alarcón-Elbal
Keyword(s):  
South African ◽  
Chikungunya Virus ◽  
Vector Competence ◽  
Temperate Climate ◽  
Southeastern Brazil ◽  
East Central ◽  
Diapausing Eggs ◽  
Cold Tolerant ◽  
Asian Lineage ◽  
Central South

Two recent researches described the spread of East/Central/South African (ECSA) lineage of chikungunya virus (CHIKV) in the Northeastern and Southeastern Brazil (Charlys da Costa et al. 2017, Cunha et al. 2017) . Initial studies in Northern Brazil, as observed in Caribbean, identified the Asian as the circulating lineage of the chikungunya. However, da Charlys da Costa et al. and Cunha et al. reported the exclusive occurrence of ECSA in two different Brazilian regions: Northeast as well as in Rio de Janeiro State (Charlys da Costa et al. 2017, Cunha et al. 2017) , suggesting that the ECSA is the predominant lineage in highly populated Brazilian areas. Despite the well-described vector competence of Aedes mosquitoes for CHIKV transmission, Aedes(Stegomyia)albopictus seems to have a greater competence for transmission of ECSA lineage compared to the Asian lineage (Vega-Rúa et al. 2015) , particularly when variable temperatures mimicking daily fluctuations of temperate climate (Vega-Rúa et al. 2015) . This statement is consistent with the fact that A albopictus has not been denounced as a vector of large outbreaks of chikungunya caused by the Asian genotype. This invasive species have capability of cold-tolerant diapausing eggs, it is paramount to establishment in temperate areas (Mitchell 1995) and new regions are invaded each year (Kraemer et al. 2015) . The predominance of the ECSA lineage in Brazil represents a potential risk of CHIKV dispersion to areas where Ae. albopictus has a broader distribution, particularly in temperate climates, including United States and Europe (Kraemer et al. 2015) , territories with intense commercial and touristic relationship with Brazil. Furthermore, the predominance of ECSA in Brazil can contributes to a better comprehension of the current distinct epidemiological scenarios between Caribbean - where explosive epidemics occurred with Aedes(Stegomyia) aegypti and Asian lineage predominated - and Brazil - with an apparent slower dispersion of CHIKV, where Ae.aegypti predominate but ECSA was prevalent linage. Both studies highlighted the importance of virological surveillance for analysis of current epidemiological scenarios and prediction of potential patterns of spreading of arboviral diseases, locally and worldwide.

scholarly journals Pathogenetic Potential Relating to Metabolic Activity in a Mouse Model of Infection with the Chikungunya Virus East/Central/South African Genotype

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 169
Author(s):  
Mya Myat Ngwe Tun ◽  
Rohitha Muthugala ◽  
Aung Kyaw Kyaw ◽  
Satoshi Shimada ◽  
Kouichi Morita ◽  
...  
Keyword(s):  
South African ◽  
Metabolic Activity ◽  
Chikungunya Virus ◽  
Type I ◽  
Pathogenic Potential ◽  
East Central ◽  
Viral Loads ◽  
Central Nervous Systems ◽  
Mouse Model Of Infection ◽  
Central South

Epidemics of the Chikungunya virus (CHIKV) from 2004 onwards were caused by the East/Central/South African (ECSA) genotype. However, the pathogenesis of the genotype infection has not been fully explained. In this study, we examined the pathogenic potential of CHIKV ECSA genotype M-30 (M-30) by comparing it with that of African genotype S-27 (S-27) in mice. Following low titer infections in type-I IFN receptor KO (A129) mice, we found that the M-30 infection caused high and acute fatality compared with the S-27 infection. M-30-infected A129 mice showed higher viral loads in their central nervous systems and peripheral organs, and increased levels of IFN-γ responses in their brains. Interestingly, M-30-infected mice did not show the hypophagia and reductions in weight which were observed in S-27-infected mice. Our observations provide a novel explanation of the pathogenic mechanisms attributed to virus proliferation, anti-type-II IFN response and metabolic activity in the CHIKV ECSA virus in mice.

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