Genome Sequences of Chikungunya Virus Strains from Bangladesh and Thailand

Pyke, Alyssa T.; McMahon, Jamie; Burtonclay, Peter; Nair, Neelima; Jong, Amanda De

doi:10.1128/mra.01452-19

Cited by 7 publications

(12 citation statements)

References 9 publications

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“…In the present study, we examined CHIKV-positive serum from Dhaka during July–December 2017 [ 11 ]. Later in 2018–2019, CHIKV transmission was observed in nearby regions simultaneously, and the number of CHIKV cases noticeably increased in travelers and locals in Myanmar and especially Thailand [ 19 , 38 , 39 , 40 ]. According to the national surveillance of Thailand, the numbers of confirmed cases were 10, 3,580, and 11,721 in 2017, 2018, and 2019, respectively [ 15 ].…”

Section: Discussionmentioning

confidence: 99%

“…Five μL of the amplified fragments were processed for library preparation by an Illumina Nextera XT kit (Illumina, San Diego, CA, USA) and the paired-end of the 2 × 250 bp sequencing reaction was conducted using the Miseq platform (Illumina, San Diego, CA, USA) according to a previously published protocol [ 18 ]. The forward and reverse short reads were imported to CLC Genomics Workbench software version 20 (Qiagen, Aarhus, Denmark) and then aligned to the MF773566-Bangladesh 2017 sequence [ 19 ] using map reads to the reference command. Finally, the consensus sequence was extracted.…”

Section: Methodsmentioning

confidence: 99%

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A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand

Phadungsombat

Imad

Rahman

et al. 2020

Viruses

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In recent decades, chikungunya virus (CHIKV) has become geographically widespread. In 2004, the CHIKV East/Central/South African (ECSA) genotype moved from Africa to Indian ocean islands and India followed by a large epidemic in Southeast Asia. In 2013, the CHIKV Asian genotype drove an outbreak in the Americas. Since 2016, CHIKV has re-emerged in the Indian subcontinent and Southeast Asia. In the present study, CHIKVs were obtained from Bangladesh in 2017 and Thailand in 2019, and their nearly full genomes were sequenced. Phylogenetic analysis revealed that the recent CHIKVs were of Indian Ocean Lineage (IOL) of genotype ECSA, similar to the previous outbreak. However, these CHIKVs were all clustered into a new distinct sub-lineage apart from the past IOL CHIKVs, and they lacked an alanine-to-valine substitution at position 226 of the E1 envelope glycoprotein, which enhances CHIKV replication in Aedes albopictus. Instead, all the re-emerged CHIKVs possessed mutations of lysine-to-glutamic acid at position 211 of E1 and valine-to-alanine at position 264 of E2. Molecular clock analysis suggested that the new sub-lineage CHIKV was introduced to Bangladesh around late 2015 and Thailand in early 2017. These results suggest that re-emerged CHIKVs have acquired different adaptations than the previous CHIKVs.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand

Phadungsombat

Imad

Rahman

et al. 2020

Viruses

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“…The patient's JEV isolate (JEV Bali 2019) was further characterised by massive parallel sequencing using the Nextera XT kit for cDNA library construction and paired-end (2 × 150 nucleotides) sequencing using the V2 mid-output kit on a NextSeq 500 machine (Illumina, San Diego, CA) as previously described [5]. A total of 16,585,742 raw sequencing reads were obtained and were processed using Geneious R10 version 10.2.6 software [6].…”

Section: Whole Genome Sequencing and Phylogenetic Analysismentioning

confidence: 99%

“…Phylogenetic analysis comparing the complete coding region (10,302 nucleotides) of JEV Bali 2019 with 242 other JEV strains (Figure 3) was performed using FastTree software and the general time-reversible nucleotide substitution model as previously described [5]. JEV Bali 2019 (GenBank accession number MT253731.1) grouped within JEV genotype IV and was most closely related to the strain JEV/sw/Bali/93/2017 isolated in Bali, Indonesia, 2017 (GenBank accession number LC461961.1) and JEV strain JKT6468 isolated in Indonesia, 1981 (GenBank accession number AY184212.1), sharing 99.23% and 95.38% nucleotide identity respectively, over the complete genome (10,970 nucleotides).…”

Section: Whole Genome Sequencing and Phylogenetic Analysismentioning

confidence: 99%

“…Midpoint rooted, approximately maximum likelihood phylogenetic tree estimated from 243 JEV complete coding region sequences (10,303 nucleotides). Tree construction was performed as previously described[5] using FastTree version 2.1.11 software and the general time reversible (GTR) nucleotide substitution model. Multiple sequence alignments were performed using the Multiple Alignment Using Fast Fourier Transform (MAFFT) program, version 7.450, and Geneious software, version 10.2.6.…”

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confidence: 99%

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A Case of Japanese Encephalitis with a Fatal Outcome in an Australian Who Traveled from Bali in 2019

Pyke¹,

Choong

Moore³

et al. 2020

TropicalMed

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A severe case of Japanese encephalitis virus (JEV) infection, resulting in fatality, occurred in an unvaccinated Australian male traveler from Bali, Indonesia, in 2019. During hospitalisation in Australia, patient cerebrospinal fluid (CSF) yielded JEV-specific IgM antibodies and RNA, and an isolate of the virus. Ongoing transmission of JEV in Bali underscores this pathogen as a public health risk and the importance of appropriate health, vaccination and mosquito avoidance advice to prospective travelers to the region.

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Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito

Pyke

Shivas

Darbro³

et al. 2021

Virus Evolution

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The Australian backyard mosquito, Aedes notoscriptus, is a highly urbanized pest species that has invaded New Zealand and the United States. Importantly, Ae. notoscriptus has been implicated as a vector of Ross River virus, a common and arthritogenic arbovirus in Australia, and is a laboratory vector of numerous other pathogenic viruses, including West Nile, yellow fever and Zika viruses. To further explore live viruses harboured by field populations of Ae. notoscriptus and, more specifically, assess the genetic diversity of its virome, we processed 495 pools, comprising a total of 6,674 female Ae. notoscriptus collected across fifteen suburbs in Brisbane, Australia, between January 2018 and May 2019. Nine virus isolates were recovered and characterised by metagenomic sequencing and phylogenetics. The principal viral family represented was Flaviviridae. Known viruses belonging to the genera Flavivirus, Orbivirus, Mesonivirus and Nelorpivirus were identified together with two novel virus species, including a divergent Thogoto-like orthomyxovirus and an insect-specific flavivirus. Among these, we recovered three Stratford virus (STRV) isolates and an isolate of Wongorr virus (WGRV), which for these viral species, is unprecedented for the geographical area of Brisbane. Thus, the documented geographical distribution of STRV and WGRV, both known for their respective medical and veterinary importance, has now been expanded to include this major urban centre. Phylogenies of the remaining five viruses, namely, Casuarina, Ngewotan, the novel Thogoto-like virus, and two new flavivirus species, suggested they are insect-specific viruses (ISVs). None of these viruses have been previously associated with Ae. notoscriptus or been reported in Brisbane. These findings exemplify the rich genetic diversity and viral abundance within the Ae. notoscriptus virome and further highlight this species as a vector of concern with the potential to transmit viruses impacting human or animal health. Considering it is a common pest and vector in residential areas, and is expanding its global distribution, ongoing surveillance, and ecological study of Ae. notoscriptus, together with mapping of its virome and phenotypic characterization of isolated viruses, is clearly warranted. Immanently, these initiatives are essential for future understanding of both the mosquito virome and the evolution of individual viral species.

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Genome Sequences of Chikungunya Virus Strains from Bangladesh and Thailand

Cited by 7 publications

References 9 publications

A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand

A Novel Sub-Lineage of Chikungunya Virus East/Central/South African Genotype Indian Ocean Lineage Caused Sequential Outbreaks in Bangladesh and Thailand

A Case of Japanese Encephalitis with a Fatal Outcome in an Australian Who Traveled from Bali in 2019

Uncovering the genetic diversity within the Aedes notoscriptus virome and isolation of new viruses from this highly urbanised and invasive mosquito

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