Enhanced Molecular Surveillance of Chikungunya Virus

ABSTRACT Outbreaks of the emerging arbovirus chikungunya virus (CHIKV) affect millions of individuals in Asia, Africa, and Latin America. Vector competence can be changed dramatically by single amino acid exchanges located predominantly within the CHIKV E1 and E2 envelope proteins, which are associa...

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Autores principales:	Carlo Fischer, Xavier de Lamballerie, Jan Felix Drexler
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	adaptive mutations alphavirus molecular epidemiology vector-borne diseases Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/33fa1bc084ee453391b0df6e763ecf5e
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spelling	oai:doaj.org-article:33fa1bc084ee453391b0df6e763ecf5e2021-11-15T15:22:27ZEnhanced Molecular Surveillance of Chikungunya Virus10.1128/mSphere.00295-192379-5042https://doaj.org/article/33fa1bc084ee453391b0df6e763ecf5e2019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00295-19https://doaj.org/toc/2379-5042ABSTRACT Outbreaks of the emerging arbovirus chikungunya virus (CHIKV) affect millions of individuals in Asia, Africa, and Latin America. Vector competence can be changed dramatically by single amino acid exchanges located predominantly within the CHIKV E1 and E2 envelope proteins, which are associated with enhanced transmissibility by anthropophilic Aedes mosquitoes. Commonly used reference assays for molecular surveillance cover only a few adaptive mutations within the envelope domains and have not been validated for all CHIKV genotypes. The recognized landscape of CHIKV adaptive mutations is thus likely incomplete. We designed two nested reverse transcription-PCR (RT-PCR) assays that cover hot spots of viral adaptation to vectors within the E1 and E2 genomic domains. Primers were designed in conserved genomic regions to allow broad usability across CHIKV genotypes. The sensitivity of both assays was at least equivalent to E1- and E2-based reference assays and robust among CHIKV genotypes at 51.4 IU/reaction (E1, 95% confidence interval [CI], 39.8 to 78.9) and 4.0 IU/reaction (E2, 95% CI, 2.0 to 7.4). Upon analysis of the complete known CHIKV genomic diversity, up to 11 nucleotide mismatches with CHIKV variants occurred under oligonucleotide binding sites of reference assays, potentially limiting assay sensitivity, whereas no critical mismatches occurred in the new assays. Specificity testing with nine alphaviruses representing all serocomplexes showed amplification of Mayaro virus and O'nyong-nyong virus by the E1-based assay, but not by the E2-based assay. The high sensitivity and specificity of the new E2-based assay may allow its diagnostic usage in resource-limited settings. The combined new assays allow improved molecular epidemiological surveillance of CHIKV globally. IMPORTANCE The life cycle of arboviruses relies on efficient infection of and transmission by arthropod vectors. Adaptation to new vectors can thus dramatically increase the geographic range of an arbovirus. Several adaptive mutations enhance chikungunya virus (CHIKV) transmissibility by different mosquito species. The appearance of those adaptive mutations has led to large-scale CHIKV outbreaks in Asia, Africa, and Europe. Molecular surveillance of circulating CHIKV strains for adaptive mutations contributes to precise risk assessments and efficient vector control and provides new insight into the evolution of vector adaptation. Existing assays for molecular CHIKV surveillance are limited by poor coverage of known adaptive mutations, low sensitivity, and cost-intensive deep sequencing approaches, preventing universal application. We developed two highly sensitive nested RT-PCR assays that cover hot spots of vector adaptation in CHIKV envelope domains. The new assays allow unprecedented molecular surveillance across all CHIKV genotypes and diagnostic use in resource-limited settings globally.Carlo FischerXavier de LamballerieJan Felix DrexlerAmerican Society for Microbiologyarticleadaptive mutationsalphavirusmolecular epidemiologyvector-borne diseasesMicrobiologyQR1-502ENmSphere, Vol 4, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	adaptive mutations alphavirus molecular epidemiology vector-borne diseases Microbiology QR1-502
spellingShingle	adaptive mutations alphavirus molecular epidemiology vector-borne diseases Microbiology QR1-502 Carlo Fischer Xavier de Lamballerie Jan Felix Drexler Enhanced Molecular Surveillance of Chikungunya Virus
description	ABSTRACT Outbreaks of the emerging arbovirus chikungunya virus (CHIKV) affect millions of individuals in Asia, Africa, and Latin America. Vector competence can be changed dramatically by single amino acid exchanges located predominantly within the CHIKV E1 and E2 envelope proteins, which are associated with enhanced transmissibility by anthropophilic Aedes mosquitoes. Commonly used reference assays for molecular surveillance cover only a few adaptive mutations within the envelope domains and have not been validated for all CHIKV genotypes. The recognized landscape of CHIKV adaptive mutations is thus likely incomplete. We designed two nested reverse transcription-PCR (RT-PCR) assays that cover hot spots of viral adaptation to vectors within the E1 and E2 genomic domains. Primers were designed in conserved genomic regions to allow broad usability across CHIKV genotypes. The sensitivity of both assays was at least equivalent to E1- and E2-based reference assays and robust among CHIKV genotypes at 51.4 IU/reaction (E1, 95% confidence interval [CI], 39.8 to 78.9) and 4.0 IU/reaction (E2, 95% CI, 2.0 to 7.4). Upon analysis of the complete known CHIKV genomic diversity, up to 11 nucleotide mismatches with CHIKV variants occurred under oligonucleotide binding sites of reference assays, potentially limiting assay sensitivity, whereas no critical mismatches occurred in the new assays. Specificity testing with nine alphaviruses representing all serocomplexes showed amplification of Mayaro virus and O'nyong-nyong virus by the E1-based assay, but not by the E2-based assay. The high sensitivity and specificity of the new E2-based assay may allow its diagnostic usage in resource-limited settings. The combined new assays allow improved molecular epidemiological surveillance of CHIKV globally. IMPORTANCE The life cycle of arboviruses relies on efficient infection of and transmission by arthropod vectors. Adaptation to new vectors can thus dramatically increase the geographic range of an arbovirus. Several adaptive mutations enhance chikungunya virus (CHIKV) transmissibility by different mosquito species. The appearance of those adaptive mutations has led to large-scale CHIKV outbreaks in Asia, Africa, and Europe. Molecular surveillance of circulating CHIKV strains for adaptive mutations contributes to precise risk assessments and efficient vector control and provides new insight into the evolution of vector adaptation. Existing assays for molecular CHIKV surveillance are limited by poor coverage of known adaptive mutations, low sensitivity, and cost-intensive deep sequencing approaches, preventing universal application. We developed two highly sensitive nested RT-PCR assays that cover hot spots of vector adaptation in CHIKV envelope domains. The new assays allow unprecedented molecular surveillance across all CHIKV genotypes and diagnostic use in resource-limited settings globally.
format	article
author	Carlo Fischer Xavier de Lamballerie Jan Felix Drexler
author_facet	Carlo Fischer Xavier de Lamballerie Jan Felix Drexler
author_sort	Carlo Fischer
title	Enhanced Molecular Surveillance of Chikungunya Virus
title_short	Enhanced Molecular Surveillance of Chikungunya Virus
title_full	Enhanced Molecular Surveillance of Chikungunya Virus
title_fullStr	Enhanced Molecular Surveillance of Chikungunya Virus
title_full_unstemmed	Enhanced Molecular Surveillance of Chikungunya Virus
title_sort	enhanced molecular surveillance of chikungunya virus
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/33fa1bc084ee453391b0df6e763ecf5e
work_keys_str_mv	AT carlofischer enhancedmolecularsurveillanceofchikungunyavirus AT xavierdelamballerie enhancedmolecularsurveillanceofchikungunyavirus AT janfelixdrexler enhancedmolecularsurveillanceofchikungunyavirus
_version_	1718427939696017408

Enhanced Molecular Surveillance of Chikungunya Virus

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