Genetic divergence of Chikungunya virus plaque variants from the Comoros Island (2005)

Wasonga, Caroline; Inoue, Satoshi; Rumberia, Cecilia; Michuki, George; Kimotho, James; Ongus, Juliette R.; Sang, Rosemary; Musila, Lillian

doi:10.1007/s11262-015-1243-4

Cited by 8 publications

(7 citation statements)

References 19 publications

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“…In protein E3, at position 23, parental isoleucine is replaced by threonine in all strains. This mutation has also been described in Indian Ocean strains [51]. Many substitutions in the E2 protein were detected (Table 3), accompanying a major adaptive mutation in E1.…”

Section: Discussionsupporting

confidence: 63%

Viral Exploration of Negative Acute Febrile Cases Observed during Chikungunya Outbreaks in Gabon

et al. 2018

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Non-malarial febrile illness outbreaks were documented in 2007 and 2010 in Gabon. After investigation, these outbreaks were attributed to the chikungunya and dengue viruses (CHIKV and DENV). However, for more than half of the samples analyzed, the causative agent was not identified. Given the geographical and ecological position of Gabon, where there is a great animal and microbial diversity, the circulation of other emerging viruses was suspected in these samples lacking aetiology. A total of 436 undiagnosed samples, collected between 2007 and 2013, and originating from 14 urban, suburban, and rural Gabonese locations were selected. These samples were used for viral isolation on newborn mice and VERO cells. In samples with signs of viral replication, cell supernatants and brain suspensions were used to extract nucleic acids and perform real-time RT-PCR targeting specific arboviruses, i.e., CHIKV, DENV, yellow fever, Rift Valley fever, and West Nile and Zika viruses. Virus isolation was conclusive for 43 samples either on newborn mice or by cell culture. Virus identification by RT-PCR led to the identification of CHIKV in 37 isolates. A total of 18 complete genomes and 19 partial sequences containing the E2 and E1 genes of CHIKV were sequenced using next-generation sequencing technology or the Sanger method. Phylogenetic analysis of the complete genomes showed that all the sequences belong to the East Central South Africa lineage. Furthermore, we identified 2 distinct clusters. The first cluster was made up of sequences from the western part of Gabon, whereas the second cluster was made up of sequences from the southern regions, reflecting the way CHIKV spread across the country following its initial introduction in 2007. Similar results were obtained when analyzing the CHIKV genes of the E2 and E1 structural proteins. Moreover, study of the mutations found in the E2 and E1 structural proteins revealed the presence of several mutations that facilitate the adaptation to the Aedes albopictus mosquito, such as E2 I211T and E1 A226V, in all the Gabonese CHIKV strains. Finally, sequencing of 6 additional viral isolates failed to lead to any conclusive identification.

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Section: Discussionsupporting

confidence: 63%

Viral Exploration of Negative Acute Febrile Cases Observed during Chikungunya Outbreaks in Gabon

et al. 2018

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“…11,12 We also observed viral variants with different plaque morphology including small plaque sizes in CHIKV primary isolate. It is curious how small plaque size variants with supposedly lower fitness were maintained in natural viral quasispecies.…”

Section: Selection Of Small Plaque Variant Of Chikvmentioning

confidence: 71%

“…15 While large plaque virus may replicate better and have higher fitness in mammalian hosts, small plaque virus may provide some selective advantage when the virus is transmitted to mosquito vector. 12 Alternating replication in mammalian host and mosquito vector provides unique selective environment and constraint for the viral quasispecies. Previously published data on another arbovirus, West Nile virus, showed that viruses from mosquitoes are more diverse than viruses from birds.…”

Section: Virulence Of Wild Type and Small Plaque Variant Of Chikvmentioning

confidence: 99%

“…However, those particular amino acid residues can be observed in other isolates as well. 12 Therefore it is not clear whether these specific sequences are required for small plaque phenotype. To get an answer for our small plaque size variant, the whole genome sequencing, sequences comparison between the variants and confirmation by reverse genetics shall be performed in the future.…”

Section: Virulence Of Wild Type and Small Plaque Variant Of Chikvmentioning

confidence: 99%

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Small plaque size variant of chikungunya primary isolate showed reduced virulence in mice

Jaimipak

Yoksan

Ubol

et al. 2017

Asian Pac J Allergy Immunol

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“…2009 ), Comoros in 2005 ( Kariuki Njenga et al. 2008 ; Wasonga et al. 2015 ), India in 2008–2013 ( Abraham et al.…”

Section: Discussionmentioning

confidence: 99%

Chikungunya virus evolution following a large 3′UTR deletion results in host-specific molecular changes in protein-coding regions

et al. 2018

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The 3′untranslated region (UTR) in alphavirus genomes functions in virus replication and plays a role in determining virus host range. However, the molecular evolution of virus UTRs is understudied compared to the evolution of protein-coding regions. Chikungunya virus (CHIKV) has the longest 3′UTR among the alphaviruses (500–700 nt), and 3′UTR length and sequence structure vary substantially among different CHIKV lineages. Previous studies showed that genomic deletions and insertions are key drivers of CHIKV 3′UTR evolution. Inspired by hypothesized deletion events in the evolutionary history of CHIKV, we used experimental evolution to examine CHIKV adaptation in response to a large 3′UTR deletion. We engineered a CHIKV mutant with a 258 nt deletion in the 3′UTR (ΔDR1/2). This deletion reduced viral replication on mosquito cells, but did not reduce replication on mammalian cells. To examine how selective pressures from vertebrate and invertebrate hosts shape CHIKV evolution after a deletion in the 3′UTR, we passaged ΔDR1/2 virus populations strictly on primate cells, strictly on mosquito cells, or with alternating primate/mosquito cell passages. We found that virus populations passaged on a single host cell line increased in fitness relative to the ancestral deletion mutant on their selected host, and viruses that were alternately passaged improved on both hosts. Surprisingly, whole genome sequencing revealed few changes in the 3′UTR of passaged populations. Rather, virus populations evolved improved fitness through mutations in protein coding regions that were associated with specific hosts.

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Genetic divergence of Chikungunya virus plaque variants from the Comoros Island (2005)

Cited by 8 publications

References 19 publications

Viral Exploration of Negative Acute Febrile Cases Observed during Chikungunya Outbreaks in Gabon

Viral Exploration of Negative Acute Febrile Cases Observed during Chikungunya Outbreaks in Gabon

Small plaque size variant of chikungunya primary isolate showed reduced virulence in mice

Chikungunya virus evolution following a large 3′UTR deletion results in host-specific molecular changes in protein-coding regions

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