Emergence of Chikungunya Virus, Pakistan, 2016-2017.
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ABSTRACT:
SUBMITTER: Badar N
PROVIDER: S-EPMC6986857 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus, which has infected millions of people in Africa, Asia, Americas, and Europe since it reemerged in India and Indian Ocean regions in 2005-2006. Starting in the middle of November 2016, CHIKV has been widely spread, and more than 4,000 cases of infections in humans were confirmed in Pakistan. Here, we report the first isolation and characterization of CHIKV from the Pakistan outbreak. Eight CHIKV strains were newly isolated from human serum samples using a cell culture procedure. A full-length genome sequence and eight complete envelope (E1) sequences of CHIKV from Pakistan were obtained in this study. Alignment of the CHIKV E1 sequences revealed that the eight new CHIKV isolates were highly homogeneous, with only two nonsynonymous substitutions found at generally conserved sites (E99 and Q235). Based on the comparison of 342 E1 sequences, the two nonsynonymous mutations were located in well-recognized domains associated with viral functions such as the cell fusion and vector specificity, suggesting their potential functional importance. Phylogenetic analysis indicated that the CHIKV strains from Pakistan originated from CHIKV circulating in the Indian region. This study helps elucidate the epidemics of CHIKV in Pakistan and also provides a foundation for studies of evolution and expansion of CHIKV in South Asia.
| S-EPMC6598907 | biostudies-literature
Project description:Chikungunya virus outbreak in Italy 2017
| PRJEB23510 | ENA
Project description:Background & objectivesChikungunya (CHIK) is a neglected, re-emerging arboviral disease. Limited information on CHIK-confirmed cases during interepidemic period is available from India. This surveillance study was conducted in Madhya Pradesh (MP), India, during the years 2016-2017, to provide information about CHIK cases.MethodsBlood samples collected from patients suspected having CHIK were tested by immunoglobulin (Ig) IgM ELISA or real time reverse transcription-polymerase chain reaction (rRT-PCR) for the detection of CHIK virus (CHIKV)-specific IgM antibodies or viral RNA, respectively. Partial envelope-1 gene sequencing was done. Clinical and demographic data were collected and analyzed.ResultsOf the 4019 samples tested, 494 (12.2%) were found positive for CHIKV infection. The positivity was detected in both rural and urban areas. The mean age of CHIK-positive cases was 33.12±18.25 yr. Headache and joint pain were the most prominent symptoms, 34.6 per cent (171/494) of the CHIK cases required hospitalization and six patients with CHIKV infection died. The East/Central/South African genotype of CHIKV was found to be circulating in the study area.Interpretation & conclusionsOur study recorded a higher CHIK positivity during 2016-2017 in comparison to earlier reports from MP, India. A high proportion of CHIK cases required hospitalization and deaths were also reported, which indicated the severity of the disease in the study area. In-depth molecular analysis of the virus and other risk factors is essential to understand the trends in disease severity.
| S-EPMC7055169 | biostudies-literature
Project description:Chikungunya virus (CHIKV) is a mosquito-borne virus that causes epidemics widely in the world especially in the tropical and subtropical regions. Phylogenetic analysis has found that the CHIKV lineages were associated with the spatial and temporal distributions, which were related to the virus adaption to the major mosquito species and their distributions. In this study, we reported the complete genome sequences of eight CHIKV isolates from the outbreak in Pakistan last year. Then we reviewed the evolutionary history using extensive phylogenetic analysis, analyzed lineage-specific substitutions in viral proteins, and characterized the spreading pathway of CHIKV strains including the Pakistani strains. The results showed that the Pakistani stains belonged to the ECSA.IOL sub-lineage and derived from India. The genetic properties of the Pakistani strains including the adaptive substitution to vectors were further characterized, and the potential risks from the occurrence of CHIKV infection in Pakistan were discussed. These results provided better understanding of CHIKV evolution and transmission in the world and revealed the possible origination of the CHIKV outbreak and epidemic in Pakistan, which would promote the disease prevention and control in the identified countries and territories with the history of CHIKV infections as well as new regions with potential risk of CHIKV outbreaks.
| S-EPMC6598911 | biostudies-literature
Project description:Chikungunya virus (CHIKV) is considered a public health problem due to its rapid spread and high morbidity. In 2016-2017 an outbreak of CHIKV was occurred in Pakistan but the data regarding the genomic diversity of CHIKV was not reported. Hence, the current study aimed to determine the genetic diversity of CHIKVs in Pakistan. A cross sectional study was carried out using sera of infected CHIKV patients (n = 1549) during the outbreak in Pakistan (2016-2018). Nucleotide sequencing of non-structural genes of CHIKV from eight isolates were performed followed by phylogenetic analysis using Bayesian method. Phylogenetic analysis suggested that the Pakistani CHIKV strains belonged to Indian Ocean Lineage (IOL) of genotype ECSA and C1.3a clade. Furthermore, the Pakistani isolates showed several key mutations (nsP2-H130Y, nsP2-E145D, nsP4-S55N and nsP4- R85G) corresponding to mutations reported in 2016 Indian strains of CHIKV. The molecular analysis revealed high evolutionary potential of CHIKV strains as well as better understanding of enhanced virulence and pathogenesis of this outbreak. The study highlights the need to continue surveillance in order to understand viral diversity over time and to devise preventive measures to limit diseases transmission in the region.
| S-EPMC8699639 | biostudies-literature
Project description:Chikungunya virus (CHIKV) causes a severe and often persistent arthralgic disease that is occasionally fatal. A mosquito-borne virus, CHIKV exists in enzootic, non-human primate cycles in Africa, but occasionally emerges into urban, human cycles to cause major epidemics. Between 1920 and 1950, and again in 2005, CHIKV emerged into India and Southeast Asia, where major urban epidemics ensued. Unlike the early introduction, the 2005 emergence was accompanied by an adaptive mutation that allowed CHIKV to exploit a new epidemic vector, Aedes albopictus, via an A226V substitution in the E1 envelope glycoprotein. However, recent reverse genetic studies indicate that lineage-specific epistatic restrictions can prevent this from exerting its phenotype on mosquito infectivity. Thus, the A. albopictus-adaptive A226V substitution that is facilitating the dramatic geographic spread CHIKV epidemics, was prevented for decades or longer from being selected in most African enzootic strains as well as in the older endemic Asian lineage.
| S-EPMC3182774 | biostudies-literature
Project description:Between late 2017 and mid-2018, a chikungunya fever outbreak occurred in Mombasa, Kenya that followed an earlier outbreak in mid-2016 in Mandera County on the border with Somalia. Using targeted Next Generation Sequencing, we obtained genomes from clinical samples collected during the 2017/2018 Mombasa outbreak. We compared data from the 2016 Mandera outbreak with the 2017/2018 Mombasa outbreak, and found that both had the Aedes aegypti adapting mutations, E1:K211E and E2:V264A. Further to the above two mutations, 11 of 15 CHIKV genomes from the Mombasa outbreak showed a novel triple mutation signature of E1:V80A, E1:T82I and E1:V84D. These novel mutations are estimated to have arisen in Mombasa by mid-2017 (2017.58, 95% HPD: 2017.23, 2017.84). The MRCA for the Mombasa outbreak genomes is estimated to have been present in early 2017 (2017.22, 95% HPD: 2016.68, 2017.63). Interestingly some of the earliest genomes from the Mombasa outbreak lacked the E1:V80A, E1:T82I and E1:V84D substitutions. Previous laboratory experiments have indicated that a substitution at position E1:80 in the CHIKV genome may lead to increased CHIKV transmissibility by Ae. albopictus. Genbank investigation of all available CHIKV genomes revealed that E1:V80A was not present; therefore, our data constitutes the first report of the E1:V80A mutation occurring in nature. To date, chikungunya outbreaks in the Northern and Western Hemispheres have occurred in Ae. aegypti inhabited tropical regions. Notwithstanding, it has been suggested that an Ae. albopictus adaptable ECSA or IOL strain could easily be introduced in these regions leading to a new wave of outbreaks. Our data on the recent Mombasa CHIKV outbreak has shown that a potential Ae. albopictus adapting mutation may be evolving within the East African region. It is even more worrisome that there exists potential for emergence of a CHIKV strain more adapted to efficient transmission by both Ae. albopictus and Ae.aegypti simultaneously. In view of the present data and history of chikungunya outbreaks, pandemic potential for such a strain is now a likely possibility in the future. Thus, continued surveillance of chikungunya backed by molecular epidemiologic capacity should be sustained to understand the evolving public health threat and inform prevention and control measures including the ongoing vaccine development efforts.
| S-EPMC7647060 | biostudies-literature
Project description:We describe a series of severe neuroinvasive infections caused by Toscana virus, identified by real-time reverse transcription PCR testing, in 8 hospitalized patients in Bucharest, Romania, during the summer seasons of 2017 and 2018. Of 8 patients, 5 died. Sequencing showed that the circulating virus belonged to lineage A.
| S-EPMC8084517 | biostudies-literature
Project description:In May 2012, the first authenticated cases of active chikungunya virus infection were detected in Champasak Province, Southern Laos. Analysis of series of human samples and mosquito specimens collected during the outbreak and over the year that followed the emergence enabled the drawing up of a map of the progression of CHIKV and the establishment of a full genetic characterization of the virus.
| S-EPMC5746231 | biostudies-literature
Project description:Chikungunya fever is a major public health issue in India. Re-emergence of chikungunya virus (CHIKV) in West Bengal was detected after 32 years in 2006. After 2010, this infection was in apparent decline, but in 2016 a massive outbreak affected the country. Present study was carried out to understand CHIKV infection dynamics during recent outbreaks in West Bengal, Eastern India and its implication on disease manifestations. Blood was collected from 641 symptomatic patients. Patients' sera were serologically diagnosed to detect presence of anti-chikungunya-IgM antibodies. Viral RNA was extracted; presence of CHIKV genome and its respective viral load was determined by real time quantitative reverse transcription-PCR (real-time qRT-PCR). Statistical analysis was performed using EPI INFO software. CHIKV infection was detected in 24.64% of symptomatic patients. Middle-aged patients (31-40 years) were predominantly affected; clinically, both arthralgia and joint-swelling were significantly prevalent among CHIKV-infected patients. Myalgia, joint-swelling, and arthralgic manifestation were found in significantly higher frequency among patients with high chikungunya viral load (> 10,000 copies/ml). Thus, this study clearly indicated the re-emergence of CHIKV in Eastern India. Significant presence of myalgia, joint swelling, and arthralgia among chikungunya patients with high viral load implied association of disease severity with viral load; requiring vigilance for proper management of infected patients as this disease is highly morbid in nature. However, in addition to chikungunya virus, other viral, bacterial, and protozoal infections also occur during post-monsoon season in India, having overlapping symptoms. Hence, continuous monitoring of these infections is required for better clinical management of patients.
| S-EPMC7058808 | biostudies-literature