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Modelling and Analyzing Virus Mutation Dynamics of Chikungunya Outbreaks.

ABSTRACT: Chikungunya fever, caused by chikungunya virus (CHIKV) and transmitted to humans by infected Aedes mosquitoes, has posed a global threat in several countries in 2015. Recent outbreaks in La Réunion, Italy and China are related with a new variant of CHIKV with shorter extrinsic incubation period in contaminated mosquitoes, but the role of this new variant on the spread of chikungunya fever is unclear. We develop a mathematical model that incorporates the virus mutation dynamics in the transmission of CHIKV among mosquitoes and humans. Our numerical simulations show that a substantial virus mutation rate combined with high virus transmission probabilities from mosquito to human, could result in sustainable chikungunya fever outbreaks. Further, we apply Markov Chain Monte Carlo sampling method to fit our model to the 2007 chikungunya fever outbreak data in North-Eastern Italy where the mutant strain was detected. We conclude that the basic reproduction number might be underestimated without considering the mutation dynamics, and our estimation shows that the basic reproduction number of the 2007 Italy outbreak was [Formula: see text]?=?2.035[95%Cl: 1.9424?-?2.1366]. Sensitivity analysis shows that the transmission rate of the mutant strain from mosquitoes to human is more influential on [Formula: see text] than the shortened extrinsic incubation period. We conclude that the virus mutation dynamics could play an important role in the transmission of CHIKV, and there is a crucial need to better understand the mutation mechanism.

SUBMITTER: Feng X

PROVIDER: S-EPMC6393467 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Modelling and Analyzing Virus Mutation Dynamics of Chikungunya Outbreaks.

Feng Xiaomei X Huo Xi X Tang Biao B Tang Sanyi S Wang Kai K Wu Jianhong J

Scientific reports 20190227 1

Chikungunya fever, caused by chikungunya virus (CHIKV) and transmitted to humans by infected Aedes mosquitoes, has posed a global threat in several countries in 2015. Recent outbreaks in La Réunion, Italy and China are related with a new variant of CHIKV with shorter extrinsic incubation period in contaminated mosquitoes, but the role of this new variant on the spread of chikungunya fever is unclear. We develop a mathematical model that incorporates the virus mutation dynamics in the transmissio ...[more]

PMID: 30814598

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Project description:BACKGROUND: CHIKV is a mosquito-borne emerging pathogen that has a major health impact in humans in tropical zones around the globe. A new variant of the virus, E1-A226V caused a large outbreak in the Indian Ocean islands and India from 2004-2007. CHIKV outbreak was initially reported in Dongguan region of Guangdong in 2010 in China, another smaller CHIKV outbreak was found in Yangjiang region of Guangdong two weeks later. The viral agent causing the two outbreaks was inferred to be the new E1-A226V variant and Yangjiang CHIKV might be introduced from Dongguan. To confirm the hypothesis and determine the origin of CHIKV causing the outbreaks, we described Yangjiang outbreak in this study, and the molecular characterization of CHIKV from Yangjiang and Dongguang outbreaks were analyzed. RESULTS: 27 clinical cases of CHIK fever were reported in outbreak in Yangjiang region. Sera sample from 12 clinical cases were collected from the outbreak, and nucleic acid and antibody tests for CHIKV were performed using Real-time RT-PCR and indirect immunofluorescence. Positive samples of Real-time RT-PCR were subjected to viral isolation. The results showed 3/12 samples positive for Real-time RT-PCR. 7/12 and 4/12 samples were positive for IgM and IgG against CHIKV respectively, two virus strains were isolated. Four viral genomes from Dongguan and Yangjiang were sequenced, characterized and phylogeneticly analyzed. Phylogenetic analysis revealed that the four seqeunced viruses had the closest relationship (99.4~99.6% identify) with the Singapore 2008 isolate belonging to the Indian ocean clade. A common mutation at the site of the E1-A226V was observed among four viruses. Four and three aa substitutions were detected in the CHIKV sequence from the Dongguan and Yangjiang outbreak strains respectively. CONCLUSION: CHIKV with an E1-A226V mutation that originated from Southeast Asia isolates caused two outbreaks in China in 2010, and originated from two different infectious sources.

Dataset Information

Modelling and Analyzing Virus Mutation Dynamics of Chikungunya Outbreaks.

Publications

Modelling and Analyzing Virus Mutation Dynamics of Chikungunya Outbreaks.

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