Two distinct lineages of chikungunya virus cocirculated in Aruba during the 2014–2015 epidemic

Phadungsombat, Juthamas; Tuekprakhon, Aekkachai; Cnops, Lieselotte; Míchiels, Johan; Berg, Riemsdijk van den; Nakayama, Emi E.; Shioda, Tatsuo; Ariën, Kevin K.; Huits, Ralph

doi:10.1016/j.meegid.2019.104129

Cited by 9 publications

(8 citation statements)

References 44 publications

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“…To determine the nucleotide sequence of the structural polyprotein of CHIKV, total extracted RNA from real-time RT-PCR-positive samples was converted into cDNA using the superscript III first-strand synthesis system (Invitrogen, Carlsbad, CA, USA). Briefly, 4 µL RNA were mixed with a specific primer [47], dNTP, buffer, MgCl 2 , and DTT following the manufacturer's protocol, and then 2 µL of 3 half cDNA was further amplified with Primestar GXL DNA polymerase (Takara, Japan) using 3 primer sets [47,48], chf18/chr24, chf20/chr24, and chf23/3RT, to obtain 3 overlapping amplified products of 2.7 kb, 1.9 kb, and 2.0 kb. The amplicons were purified, cleaned (Nucleospin, MACHEREY-NAGEL, Germany), and sequenced (Macrogen, Seoul, Korea) using the primers chr20, chr21, chr22, chf21, chf22, chf24, and chf25 [48].…”

Section: Structural Polyprotein Region Sequencing and Phylogenetic Analysismentioning

confidence: 99%

“…Briefly, 4 µL RNA were mixed with a specific primer [47], dNTP, buffer, MgCl 2 , and DTT following the manufacturer's protocol, and then 2 µL of 3 half cDNA was further amplified with Primestar GXL DNA polymerase (Takara, Japan) using 3 primer sets [47,48], chf18/chr24, chf20/chr24, and chf23/3RT, to obtain 3 overlapping amplified products of 2.7 kb, 1.9 kb, and 2.0 kb. The amplicons were purified, cleaned (Nucleospin, MACHEREY-NAGEL, Germany), and sequenced (Macrogen, Seoul, Korea) using the primers chr20, chr21, chr22, chf21, chf22, chf24, and chf25 [48]. The obtained sequences were aligned to the reference CHIKV genotype African strain S27 (NC_004162.2) in AliView V1.26 [49], and the consensus sequence of the entire structural polyprotein region (3747 bp) was manually extracted and deposited in GenBank (Accession number LC598202-LC598210).…”

Section: Structural Polyprotein Region Sequencing and Phylogenetic Analysismentioning

confidence: 99%

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Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases during the 2019 Outbreak in Thailand

et al. 2021

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Chikungunya virus is an Alphavirus belonging to the family Togaviridae that is transmitted to humans by an infected Aedes mosquito. Patients develop fever, inflammatory arthritis, and rash during the acute stage of infection. Although the illness is self-limiting, atypical and severe cases are not uncommon, and 60% may develop chronic symptoms that persist for months or even for longer durations. Having a distinct periodical epidemiologic outbreak pattern, chikungunya virus reappeared in Thailand in December 2018. Here, we describe a cohort of acute chikungunya patients who had presented to the Bangkok Hospital for Tropical Diseases during October 2019. Infection was detected by a novel antigen kit and subsequently confirmed by real-time RT-PCR using serum collected at presentation to the Fever Clinic. Other possible acute febrile illnesses such as influenza, dengue, and malaria were excluded. We explored the sequence of clinical manifestations at presentation during the acute phase and associated the viral load with the clinical findings. Most of the patients were healthy individuals in their forties. Fever and arthralgia were the predominant clinical manifestations found in this patient cohort, with a small proportion of patients with systemic symptoms. Higher viral loads were associated with arthralgia, and arthralgia with the involvement of the large joints was more common in female patients.

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Section: Structural Polyprotein Region Sequencing and Phylogenetic Analysismentioning

confidence: 99%

Section: Structural Polyprotein Region Sequencing and Phylogenetic Analysismentioning

confidence: 99%

Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases during the 2019 Outbreak in Thailand

et al. 2021

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“…Two overlapping amplified DNA fragments covering the full genome of CHIKV were prepared, quantified, and normalized to 0.2 ng/µL using a Qubit fluorometer (Themo Fisher Scientific, MA, USA). 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.…”

Section: Chikv Genome Sequencingmentioning

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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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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“…To determine the nucleotide sequence of the structural polyprotein of CHIKV, total extracted RNA from real-time RT-PCR-positive samples was converted into cDNA using the superscript III first-strand synthesis system (Invitrogen, USA). Briefly, 4µL RNA were mixed with a specific primer (87), dNTP, buffer, MgCl2, and DTT following the manufacturer's protocol, and then 2 µL of 3' half cDNA was further amplified with Primestar GXL DNA polymerase (Takara, Japan) using 3 primer sets (87,88), chf18/chr24, chf20/chr24, and chf23/3RT, to obtain 3 overlapping amplified products of 2.7 kb, 1.9 kb, and 2.0 kb. The amplicons were purified, cleaned (Nucleospin, MA-CHEREY-NAGEL, Germany), and sequenced (Macrogen, Seoul, Korea) using the primers chr20, chr21, chr22, chf21, chf22, chf24, and chf25 (88).…”

Section: Structural Polyprotein Region Sequencing and Phylogenetic Anmentioning

confidence: 99%

Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases During the 2019 Outbreak in Thailand

Imad¹,

Phadungsombat²,

Nakayama³

et al. 2020

Preprint

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Chikungunya virus is an Alphavirus belonging to the family Togaviridae that is transmitted to humans by an infected Aedes mosquito. Patients develop fever, inflammatory arthritis, and rash during the acute stage of infection. Although the illness is self-limiting, atypical and severe cases are not uncommon, and 60% may develop chronic symptoms that persist for months or even for longer durations. Having a distinct periodical epidemiologic outbreak pattern, chikungunya virus reappeared in Thailand in December 2018. Here, we describe a cohort of acute chikungunya patients who had presented to the Bangkok Hospital for Tropical Diseases during October 2019. Infection was confirmed by real-time RT-PCR using serum collected at presentation to the Fever Clinic. Other possible acute febrile illnesses such as influenza, dengue, and malaria were excluded. We explored the sequence of clinical manifestations at presentation during the acute phase and associated the viral load with the clinical findings. Most of the patients were healthy individuals in their forties. Fever and arthralgia were the predominant clinical manifestations found in this patient cohort, with a small proportion of patients with systemic symptoms. Higher viral loads were associated with arthralgia, and arthralgia with the involvement of the large joints was more common in female patients

show abstract

Two distinct lineages of chikungunya virus cocirculated in Aruba during the 2014–2015 epidemic

Cited by 9 publications

References 44 publications

Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases during the 2019 Outbreak in Thailand

Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases during the 2019 Outbreak in Thailand

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

Chikungunya Manifestations and Viremia in Patients Who Presented to the Fever Clinic at Bangkok Hospital for Tropical Diseases During the 2019 Outbreak in Thailand

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