Chikungunya emergency in China: microevolution and genetic analysis for a local outbreak

Lü, Xi; Li, Xiaobo; Mo, Ziyao; Jin, Fang; Wang, Boliang; Huang, Junfeng; Huang, Jicheng; Zhao, Hongbo; Shi, Lei

doi:10.1007/s11262-013-0991-2

Cited by 16 publications

(14 citation statements)

References 33 publications

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“…All the sequenced CHIKV strains clustered within the ECSA genotype. These sequences showed 100% similarity in the analyzed regions to sequences reported from China in 2012 . In addition, the study sequences were found to be 99% similar with samples reported from France and Hyderabad, India .…”

Section: Discussionsupporting

confidence: 67%

Molecular characterization of dengue and chikungunya virus strains circulating in New Delhi, India

Afreen

Deeba

Khan

et al. 2014

Microbiology and Immunology

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Dengue and chikungunya are acute viral infections with overlapping clinical symptoms. Both diseases are transmitted by common mosquito vectors resulting in their co-circulation in a region. Molecular and serological tests specific for both dengue and chikungunya infections were performed on 87 acute phase blood samples collected from patients with suspected dengue/chikungunya infections in Delhi from September to December, 2011. RT-PCR and IgM ELISA were performed to detect dengue virus (DENV) and chikungunya virus (CHIKV). NS1 and IgG ELISA were also performed to detect DENV specific antigen and secondary DENV infection. DENV infection was detected in 49%, CHIKV infection in 29% and co-infection with DENV and CHIKV in 10% of the samples by RT-PCR. DENV serotypes 1, 2 and 3 were detected in this study. Nine DENV-1 strains, six DENV-2 strains and 20 CHIKV strains were characterized by DNA sequencing and phylogenetic analysis of their respective envelope protein genes. DENV-1 strains grouped in the American African genotype, DENV-2 strains in the Cosmopolitan genotype and CHIKV strains in the East Central South African genotype by phylogenetic analysis. This is one of the few studies reporting the phylogeny of two dengue virus serotypes (DENV-1 and DENV-2) and CHIKV. Surveillance and monitoring of DENV and CHIKV strains are important for design of strategies to control impending epidemics.

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Section: Discussionsupporting

confidence: 67%

Molecular characterization of dengue and chikungunya virus strains circulating in New Delhi, India

Afreen

Deeba

Khan

et al. 2014

Microbiology and Immunology

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“…The Kenyan isolates shared similarity with the imported isolates in China which had a 90% nucleotide identity related to the ECSA within Indian Ocean lineage [ 43 ]. Detection of similar isolates over wide geographical areas shows how fast and wide impacts can be felt from the countries where the outbreaks originally started [ 13 ].…”

Section: Discussionmentioning

confidence: 99%

Human and entomologic investigations of chikungunya outbreak in Mandera, Northeastern Kenya, 2016

et al. 2018

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Chikungunya is a reemerging vector borne pathogen associated with severe morbidity in affected populations. Lamu, along the Kenyan coast was affected by a major chikungunya outbreak in 2004. Twelve years later, we report on entomologic investigations and laboratory confirmed chikungunya cases in northeastern Kenya. Patient blood samples were received at the Kenya Medical Research Institute (KEMRI) viral hemorrhagic fever laboratory and the immunoglobulin M enzyme linked immunosorbent assay (IgM ELISA) was used to test for the presence of IgM antibodies against chikungunya and dengue. Reverse transcription polymerase chain reaction (RT-PCR) utilizing flavivirus, alphavirus and chikungunya specific primers were used to detect acute infections and representative PCR positive samples sequenced to confirm the circulating strain. Immature mosquitoes were collected from water-holding containers indoors and outdoors in the affected areas in northeastern Kenya. A total of 189 human samples were tested; 126 from Kenya and 63 from Somalia. 52.9% (100/189) tested positive for Chikungunya virus (CHIKV) by either IgM ELISA or RT-PCR. Sequence analysis of selected samples revealed that the virus was closely related to that from China (2010). 29% (55/189) of the samples, almost all from northeastern Kenya or with a history of travel to northern Kenya, tested positive for dengue IgM antibodies. Entomologic risk assessment revealed high house, container and Breteau indices of, 14.5, 41.9 and 17.1% respectively. Underground water storage tanks were the most abundant, 30.1%, of which 77.4% were infested with Aedes aegypti mosquitoes. These findings confirm the presence of active chikungunya infections in the northeastern parts of Kenya. The detection of dengue IgM antibodies concurrently with chikungunya virus circulation emphasizes on the need for improved surveillance systems and diagnostic algorithms with the capacity to capture multiple causes of arbovirus infections as these two viruses share common vectors and eco-systems. In addition sustained entomological surveillance and vector control programs targeting most productive containers are needed to monitor changes in vector densities, for early detection of the viruses and initiate vector control efforts to prevent possible outbreaks.

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“…The ECSA strains are presently circulating in many Asian countries namely India, Sri Lanka, Bhutan, China, Singapore, Cambodia and Vietnam that originated from a cluster of the epidemic strains [45][46][47][48][49]. The other branch of the epidemic strains diverged into the sequences reported in recent years from Thailand, Sri Lanka and American regions (including Brazil, Mexico and USA).…”

Section: Epidemiology and Infectionmentioning

confidence: 99%

Global transmission and evolutionary dynamics of the Chikungunya virus

et al. 2020

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Chikungunya virus (CHIKV) is a re-emerging pathogen of global importance. We attempted to gain an insight into the organisation, distribution and mutational load of the virus strains reported from different parts of the world. We describe transmission dynamics and genetic characterisation of CHIKV across the globe during the last 65 years from 1952 to 2017. The evolutionary pattern of CHIKV was analysed using the E1 protein gene through phylogenetic, Bayesian and Network methods with a dataset of 265 sequences from various countries. The time to most recent common ancestor of the virus was estimated to be 491 years ago with an evolutionary rate of 2.78 × 10−4 substitutions/site/year. Genetic characterisation of CHIKV strains was carried out in terms of variable sites, selection pressure and epitope mapping. The neutral selection pressure on the E1 gene of the virus suggested a stochastic process of evolution. We identified six potential epitope peptides in the E1 protein showing substantial interaction with human MHC-I and MHC-II alleles. The present study augments global epidemiological and population dynamics of CHIKV warranting undertaking of appropriate control measures. The identification of epitopic peptides can be useful in the development of epitope-based vaccine strategies against this re-emerging viral pathogen.

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Chikungunya emergency in China: microevolution and genetic analysis for a local outbreak

Cited by 16 publications

References 33 publications

Molecular characterization of dengue and chikungunya virus strains circulating in New Delhi, India

Molecular characterization of dengue and chikungunya virus strains circulating in New Delhi, India

Human and entomologic investigations of chikungunya outbreak in Mandera, Northeastern Kenya, 2016

Global transmission and evolutionary dynamics of the Chikungunya virus

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