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Jamal Z, Haider SA, Hakim R, Humayun F, Farooq MU, Ammar M, Afrough B, Inamdar L, Salman M, Umair M. Serotype and genomic diversity of dengue virus during the 2023 outbreak in Pakistan reveals the circulation of genotype III of DENV-1 and cosmopolitan genotype of DENV-2. J Med Virol 2024; 96:e29727. [PMID: 38864343 DOI: 10.1002/jmv.29727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/13/2024]
Abstract
Dengue, a mosquito-borne viral disease, poses a significant public health challenge in Pakistan, with a significant outbreak in 2023, prompting our investigation into the serotype and genomic diversity of the dengue virus (DENV). NS-1 positive blood samples from 153 patients were referred to the National Institute of Health, Pakistan, between July and October 2023. Among these, 98 (64.1%) tested positive using multiplex real-time PCR, with higher prevalence among males (65.8%) and individuals aged 31-40. Serotyping revealed DENV-1 as the predominant serotype (84.7%), followed by DENV-2 (15.3%). Whole-genome sequencing of 18 samples (DENV-1 = 17, DENV-2 = 01) showed that DENV-1 (genotype III) samples were closely related (>99%) to Pakistan outbreak samples (2022), and approx. > 98% with USA (2022), Singapore and China (2016), Bangladesh (2017), and Pakistan (2019). The DENV-2 sequence (cosmopolitan genotype; clade IVA) shared genetic similarity with Pakistan outbreak sequences (2022), approx. > 99% with China and Singapore (2018-2019) and showed divergence from Pakistan sequences (2008-2013). No coinfection with dengue serotypes or other viruses were observed. Comparisons with previous DENV-1 sequences highlighted genetic variations affecting viral replication efficiency (NS2B:K55R) and infectivity (E:M272T). These findings contribute to dengue epidemiology understanding and underscore the importance of ongoing genomic surveillance for future outbreak responses in Pakistan.
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Affiliation(s)
- Zunera Jamal
- National Institutes of Health, Islamabad, Pakistan
| | | | - Rabia Hakim
- National Institutes of Health, Islamabad, Pakistan
| | | | | | | | - Babak Afrough
- New Variant Assessment Platform, UK Health Security Agency, London, UK
| | - Leena Inamdar
- New Variant Assessment Platform, UK Health Security Agency, London, UK
| | | | - Massab Umair
- National Institutes of Health, Islamabad, Pakistan
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Genomic Characterization of Dengue Virus Outbreak in 2022 from Pakistan. Vaccines (Basel) 2023; 11:vaccines11010163. [PMID: 36680008 PMCID: PMC9867254 DOI: 10.3390/vaccines11010163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/23/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Pakistan, a dengue-endemic country, has encountered several outbreaks during the past decade. The current study aimed to explore the serotype and genomic diversity of dengue virus responsible for the 2022 outbreak in Pakistan. From August to October 2022, NS-1 positive blood samples (n = 343) were collected from dengue patients, among which, (85%; n = 293) were positive based on RT-PCR. In terms of gender and age, dengue infection was more prevalent in male patients (63%; n = 184), with more adults (21-30 years; n = 94) being infected. The serotyping results revealed DENV-2 to be the most predominant serotype (62%; n = 183), followed by DENV-1 (37%; n = 109) and DENV-3 (0.32%; n = 1). Moreover, a total of 10 samples (DENV-2; n = 8, DENV-1; n = 2) were subjected to whole-genome sequencing. Among these, four were collected in early 2022, and six were collected between August and October 2022. Phylogenetic analysis of DENV-2 sequenced samples (n = 8) revealed a monophyletic clade of cosmopolitan genotype IVA, which is closely related to sequences from China and Singapore 2018, and DENV-1 samples (n = 2) show genotype III, which is closely related to Pakistan isolates from 2019. We also reported the first whole genome sequence of a coinfection case (DENV1-DENV2) in Pakistan detected through a meta-genome approach. Thus, dengue virus dynamics reported in the current study warrant large-scale genomic surveillance to better respond to future outbreaks.
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Instability of the NS1 Glycoprotein from La Reunion 2018 Dengue 2 Virus (Cosmopolitan-1 Genotype) in Huh7 Cells Is Due to Lysine Residues on Positions 272 and 324. Int J Mol Sci 2021; 22:ijms22041951. [PMID: 33669407 PMCID: PMC7920422 DOI: 10.3390/ijms22041951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022] Open
Abstract
La Reunion island in the South West Indian Ocean is now endemic for dengue following the introduction of dengue virus serotype 2 (DENV-2) cosmopolitan-I genotype in 2017. DENV-2 infection causes a wide spectrum of clinical manifestations ranging from flu-like disease to severe dengue. The nonstructural glycoprotein 1 (NS1) has been identified as playing a key role in dengue disease severity. The intracellular NS1 exists as a homodimer, whereas a fraction is driven towards the plasma membrane or released as a soluble hexameric protein. Here, we characterized the NS1 glycoproteins from clinical isolates DES-14 and RUN-18 that were collected during the DENV-2 epidemics in Tanzania in 2014 and La Reunion island in 2018, respectively. In relation to hepatotropism of the DENV, expression of recombinant DES-14 NS1 and RUN-18 NS1 glycoproteins was compared in human hepatoma Huh7 cells. We observed that RUN-18 NS1 was poorly stable in Huh7 cells compared to DES-14 NS1. The instability of RUN-18 NS1 leading to a low level of NS1 secretion mostly relates to lysine residues on positions 272 and 324. Our data raise the issue of the consequences of a defect in NS1 stability in human hepatocytes in relation to the major role of NS1 in the pathogenesis of the DENV-2 infection.
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Calvez E, Somlor S, Viengphouthong S, Balière C, Bounmany P, Keosenhom S, Caro V, Grandadam M. Rapid genotyping protocol to improve dengue virus serotype 2 survey in Lao PDR. PLoS One 2020; 15:e0237384. [PMID: 32764809 PMCID: PMC7413503 DOI: 10.1371/journal.pone.0237384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 12/30/2022] Open
Abstract
Dengue fever is one of the major public health problems in Lao PDR. Over the last decade, dengue virus (DENV) epidemics were characterized by a novel predominant serotype accompanied by at least two other serotypes. Since 2008, DENV-2 circulated at a low level in Lao PDR but its epidemiologic profile changed at the end of 2018. Indeed, the number of confirmed DENV-2 cases suddenly increased in October 2018 and DENV-2 became predominant at the country level in early 2019. We developed a Genotype Screening Protocol (GSP) to determine the origin(s) of the Lao DENV-2 and study their genetic polymorphism. With a good correlation with full envelope gene sequencing data, this molecular epidemiology tool evidence the co-circulation of two highly polymorphic DENV-2 genotypes, i.e. Asian I and Cosmopolitan genotypes, over the last five years, suggesting multiple introductions of DENV-2 in the country. GSP approach provides relevant first line information that may help countries with limited laboratory resources to reinforce their capabilities to DENV-2 and to follow the epidemics progresses and assess situations at the regional level.
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Affiliation(s)
- Elodie Calvez
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
- * E-mail:
| | - Somphavanh Somlor
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
| | | | | | | | - Sitsana Keosenhom
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
| | | | - Marc Grandadam
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
- Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
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Suzuki K, Phadungsombat J, Nakayama EE, Saito A, Egawa A, Sato T, Rahim R, Hasan A, Lin MYC, Takasaki T, Rahman M, Shioda T. Genotype replacement of dengue virus type 3 and clade replacement of dengue virus type 2 genotype Cosmopolitan in Dhaka, Bangladesh in 2017. INFECTION GENETICS AND EVOLUTION 2019; 75:103977. [PMID: 31351235 DOI: 10.1016/j.meegid.2019.103977] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/24/2019] [Accepted: 07/22/2019] [Indexed: 01/18/2023]
Abstract
Dengue is a mosquito-borne disease that has spread to >100 countries and is caused by the dengue virus (DENV), which belongs to the Flavivirus genus of the family Flaviviridae. DENV comprises 4 serotypes (DENV-1 to -4), and each serotype is further divided into distinct genotypes. In India, it is reported that all 4 serotypes of DENV co-circulate. Although Bangladesh is a neighboring country of India, very few reports have published DENV sequence data for the country, especially after 2012. To understand the current distribution of DENV genotypes in Bangladesh, we determined the nucleotide sequences of envelope regions obtained from 58 DENV-positive patients diagnosed at Apollo Hospitals Dhaka during the period between September 2017 and February 2018. We found 5 DENV-1, 47 DENV-2, and 6 DENV-3 serotypes. A phylogenetic analysis of the obtained viral sequences revealed that DENV-3 genotype I was present instead of DENV-3 genotype II, which was predominant in Bangladesh between 2000 and 2009. Furthermore, we found two distinct lineages of the Cosmopolitan genotype of DENV-2, one of which was closely related to strains from Southeast Asia and has never been reported previously in Bangladesh. These results indicated that DENVs in Bangladesh have increased in genotypic diversity and suggest that the DENV genotypic shift observed in other Asian countries also might have been taking place in Bangladesh.
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Affiliation(s)
- Keita Suzuki
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan; TANAKA Kikinzoku Kogyo K.K., 2-73, Shinmachi, Hiratsuka, Kanagawa 254-0076, Japan
| | - Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases, Mahidol University, 420/6 Ratchawithi road, Ratchathewi, Bangkok 10400, Thailand
| | - Emi E Nakayama
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Akatsuki Saito
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Akio Egawa
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tairyu Sato
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Rummana Rahim
- Apollo Hospitals Dhaka, Plot-81, Block-E, Bashundhara R/A, Dhaka 1229, Bangladesh
| | - Abu Hasan
- Apollo Hospitals Dhaka, Plot-81, Block-E, Bashundhara R/A, Dhaka 1229, Bangladesh
| | - Marco Yung-Cheng Lin
- Department of Medical Research, Mackay Memorial Hospital, No. 45, Minsheng Rd., Tamsui District, New Taipei City 25160, Taiwan
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, 1-3-1 Shimomachiya, Chigasaki, Kanagawa 253-0087, Japan
| | - Mizanur Rahman
- Apollo Hospitals Dhaka, Plot-81, Block-E, Bashundhara R/A, Dhaka 1229, Bangladesh
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan; Mahidol-Osaka Center for Infectious Diseases, Mahidol University, 420/6 Ratchawithi road, Ratchathewi, Bangkok 10400, Thailand
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Ali A, Fatima Z, Wahid B, Rafique S, Idrees M. Cosmopolitan A1 lineage of dengue virus serotype 2 is circulating in Pakistan: A study from 2017 dengue viral outbreak. J Med Virol 2019; 91:1909-1917. [PMID: 31273791 DOI: 10.1002/jmv.25537] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 05/14/2019] [Indexed: 11/10/2022]
Abstract
Dengue viral infection has become a challenge in tropical and subtropical countries where dengue virus is endemic. Its epidemics are occurring at higher rates amid its circulation throughout the year. Since the first documented outbreak in Pakistan in 1994, this region has reported many sporadic cases and epidemics. There is availability of small scale demographic and epidemiological studies on dengue viral infection in Pakistan. The year 2017 witnessed a huge dengue outbreak in Peshawar city of Pakistan with 69 deaths and 24 807 laboratory-confirmed cases. We suspect that the circulation of a different lineage or genotype could be responsible for the enhanced number of infected patients in Pakistan's 2017 outbreak since previous studies have already described this phenomenon in other countries. For this, we collected 1447 suspected blood samples and their epidemiological data. After serotyping through polymerase chain reaction nine samples of Dengue virus2 (DENV2) were randomly selected and were subjected to Sanger's sequencing for genotyping analysis. The mean distance, genetic diversity, and phylogenetic analysis were carried out using K2 model. The phylogenetic analysis split Pakistani isolates into two lineages, the sequences from 2017 outbreak in Peshawar grouped within A1 lineage of cosmopolitan genotype (IV) of DENV2. The difference in distance, genetic diversity, and amino acids composition strongly back the results that the new lineage is circulating in the region. This is significant as Pakistan is struggling to control dengue epidemics which have caused much loss in both monetary and health sectors.
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Affiliation(s)
- Amjad Ali
- Department of Genetics, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan.,Molecular Virology Laboratory, Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Zareen Fatima
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Braira Wahid
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Shazia Rafique
- Divison of Virology, Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Divison of Virology, Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
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Dias M, Pattabiraman C, Siddappa S, Gowda M, Shet A, Smith D, Muehlemann B, Tamma K, Solomon T, Jones T, Krishna S. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum. Wellcome Open Res 2019; 3:44. [PMID: 30167467 PMCID: PMC6085601 DOI: 10.12688/wellcomeopenres.14438.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2019] [Indexed: 12/02/2022] Open
Abstract
Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine. Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.
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Affiliation(s)
- Mary Dias
- St. John's Medical College and Hospital, Bangalore, 560034, India
| | - Chitra Pattabiraman
- National Institute of Mental Health and Neurosciences, India, Bangalore, 560029, India
| | - Shilpa Siddappa
- Centre for Cellular and Molecular Platforms, Bangalore, 560065, India
| | - Malali Gowda
- Trans-Disciplinary University, Foundation for Revitalization of Local Health Traditions, Bangalore, 560064, India
| | - Anita Shet
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Barbara Muehlemann
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | | | - Tom Solomon
- Institute of Infection and Global Health, and National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK
| | - Terry Jones
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
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Kar M, Nisheetha A, Kumar A, Jagtap S, Shinde J, Singla M, M S, Pandit A, Chandele A, Kabra SK, Krishna S, Roy R, Lodha R, Pattabiraman C, Medigeshi GR. Isolation and molecular characterization of dengue virus clinical isolates from pediatric patients in New Delhi. Int J Infect Dis 2018; 84S:S25-S33. [PMID: 30528666 DOI: 10.1016/j.ijid.2018.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVE To characterize the in vitro replication fitness, viral diversity, and phylogeny of dengue viruses (DENV) isolated from Indian patients. METHODS DENV was isolated from whole blood collected from patients by passaging in cell culture. Passage 3 viruses were used for growth kinetics in C6/36 mosquito cells. Parallel efforts also focused on the isolation of DENV RNA from plasma samples of the same patients, which were processed for next-generation sequencing. RESULTS It was possible to isolate 64 clinical isolates of DENV, mostly DENV-2. Twenty-five of these were further used for growth curve analysis in vitro, which showed a wide range of replication kinetics. The highest viral titers were associated with isolates from patients with dengue with warning signs and severe dengue cases. Full genome sequences of 21 DENV isolates were obtained. Genome analysis mapped the circulating DENV-2 strains to the Cosmopolitan genotype. CONCLUSIONS The replication kinetics of isolates from patients with mild or severe infection did not differ significantly, but the viral titers varied by two orders of magnitude between the isolates, suggesting differences in replication fitness among the circulating DENV-2.
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Affiliation(s)
- Meenakshi Kar
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amul Nisheetha
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Anuj Kumar
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Suraj Jagtap
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Jitendra Shinde
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Mohit Singla
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Saranya M
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, ICGEB Campus, New Delhi, India
| | - Sushil K Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sudhir Krishna
- National Centre for Biological Sciences, TIFR, Bengaluru, India
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India; Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India; Center for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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Borkakoty B, Das M, Sarma K, Jakharia A, Das PK, Bhattacharya C, Apum B, Biswas D. Molecular characterisation and phylogenetic analysis of dengue outbreak in Pasighat, Arunachal Pradesh, Northeast India. Indian J Med Microbiol 2018; 36:37-42. [PMID: 29735824 DOI: 10.4103/ijmm.ijmm_17_30] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background and Objectives Dengue is one of the most prevalent arboviral diseases in the world with 390 million dengue infections per year. In this study, we report the molecular characterisation of dengue outbreak in Pasighat, Arunachal Pradesh, Northeast India during 2015. Subjects and Methods : A total of 613 dengue-suspected cases were screened for dengue virus by dengue NS1 Ag and anti-dengue IgM antibody depending on the duration of sample collection and onset of symptom. Further, molecular characterisation was done by amplifying the C-PrM region by real-time polymerase chain reaction followed by phylogenetic analysis. Results Molecular characterisation revealed that the dengue outbreak was predominantly due to dengue virus serotype-1 (DENV-1) (90.9%) while DENV-2 was detected in 7.5% of samples. Co-infection of DENV-1 and DENV-2 was detected in one case. Phylogenetic analysis of the DENV-1 strains with the prototype revealed that the DENV-1 strains were grouped within genotype III. Similarly, DENV-2 strains were clustered within genotype IV. The study revealed a change in the predominant serotype in recent years with DENV-3 in 2012 to DENV-1, 2, 3 and 4 in 2014 to DENV-1 in 2015 in the study region. A unique L24M mutation was observed in the DENV-1 strains of Arunachal Pradesh which was absent in all the circulating strains in India except one strain from the state of Kerala in South India. Marked variation within the DENV-2 strains was observed at A102V and I163V in one strain similar to earlier circulating isolates in India. Conclusions The present study reveals a shift in the serotype dominance in the study region. As serotype shifts and secondary infection with a heterologous DENV serotype are frequently associated with disease severity, there is an urgent need for sustained monitoring of the circulating serotypes and enhanced surveillance operations, especially in the monsoon and post-monsoon periods to prevent large-scale, severe dengue outbreaks in this region.
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Affiliation(s)
| | - Mandakini Das
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
| | - Kishore Sarma
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
| | - Aniruddha Jakharia
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
| | - Palash Kumar Das
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
| | | | - Basumoti Apum
- Department of Microbiology, General Hospital, Pasighat, East Siang, Arunachal Pradesh, India
| | - Dipankar Biswas
- ICMR- Regional Medical Research Centre, N. E. Region, Dibrugarh, Assam, India
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Khan J, Khan I, Ghaffar A, Khalid B. Epidemiological trends and risk factors associated with dengue disease in Pakistan (1980-2014): a systematic literature search and analysis. BMC Public Health 2018; 18:745. [PMID: 29907109 PMCID: PMC6003098 DOI: 10.1186/s12889-018-5676-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/05/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Dengue is becoming more common in Pakistan with its alarming spreading rate. A historical review needs to be carried out to find the root causes of dengue dynamics, the factors responsible for its spread and lastly to formulate future strategies for its control. METHODS We searched (January, 2015) all the published literature between 1980 and 2014 to determine spread/burden of dengue disease in Pakistan. RESULTS A total of 81 reports were identified, showing high numbers of dengue cases in 2010, 2011, and 2013. The tendency of dengue to occur in younger than in older age groups was evident throughout the survey period and all four serotypes were recorded, with DENV1 the least common. Most dengue hemorrhagic fever (DHF) cases fell in the 20-45 years age range. High frequencies tended to be observed first in the Southern coastal region characterized by mild winters and humid warm summers and then the disease progressed towards the lowland areas of the Indus plain with cool winters, hot summers and monsoon rainfall. Based on this survey, new risk maps and infection estimates were identified reflecting public health burden imposed by dengue at the national level. CONCLUSIONS Our study showed that dengue is common in the three provinces of Pakistan, i.e., Khyber Pakhtunkhwa (KP), Punjab and Sindh. Based on the literature review as well as on our study analysis the current expansion of dengue seems multifactorial and may include climate change, virus evolution, and societal factors such as rapid urbanization, population growth and development, socioeconomic factors, as well as global travel and trade. Due to inadequate remedial strategies, effective vector control measures are essential to target the dengue vector mosquito where high levels of human-vector contact occur. The known social, economic, and disease burden of dengue is alarming globally and it is evident that the wider impact of this disease is grossly underestimated. An international multi-sectoral response, outlined in the WHO Global Strategy for Dengue Prevention and Control, 2012-2020, is now essential to reduce the significant influence of this disease in Dengue endemic areas. Overall gaps were identified in knowledge around seroprevalence, dengue incidence, vector control, genotype evolution and age-stratified serotype circulation.
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Affiliation(s)
- Jehangir Khan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 Guangdong China
- Sun Yat-sen University-Michigan State University Joint Center of Vector Control for Tropical Diseases, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 Guangdong China
- Department of Zoology, Abdul Wali Khan University Mardan (AWKUM), Mardan, Khyber Pakhtunkhwa Pakistan
- Key Laboratory of Tropical Diseases and Control of the Ministry of Education, Guangzhou, 510080 China
| | - Inamullah Khan
- Nuclear Institute for Food and Agriculture (NIFA), Peshawar, Khyber Pakhtunkhwa Pakistan
| | - Abdul Ghaffar
- Department of Meteorology, COMSATS University (CUI), Islamabad, Pakistan
| | - Bushra Khalid
- Evolution and Ecology Program, International Institute for Applied Systems Analysis, Laxenburg, Austria
- Earth System Physics, The Abdus Salam, International Centre for Theoretical Physics, Trieste, Italy
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11
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Khan J, Ghaffar A, Khan SA. The changing epidemiological pattern of Dengue in Swat, Khyber Pakhtunkhwa. PLoS One 2018; 13:e0195706. [PMID: 29689060 PMCID: PMC5916521 DOI: 10.1371/journal.pone.0195706] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 03/28/2018] [Indexed: 11/18/2022] Open
Abstract
Background Pakistan is suffering from dengue fever since 1994. In the country, major dengue outbreaks have been documented in 2010, 2011 and 2013 in Punjab (Lahore) and Sindh (Karachi) Provinces. District Swat was hit for the first time by dengue virus in 2013, claiming 57 deaths and 8000 morbidities. The molecular and entomological aspects along with the ecological and social context of the dengue outbreaks were investigated in this study. Method In addition to entomological survey, the data collected from patients' files (Saidu Sharif Teaching Hospital, Swat) and by directly questioning the patients (field data) was analyzed for epidemiological trends, molecular identification (RT-PCR based serotyping of DENV), clinical profile, socioeconomic status (SES) and demographic features. Results The peak prevalence of dengue was documented in September (56% in 2013, 38% in 2014) and October (33% in 2013, 24% in 2014), whereas in 2015, in October (54.5%) and November (30.5%). The serotype 3 (≤60%) and serotype 2 (≤40%) were found dominant in the area. Among the reported patients (5513), 69% were males and 31% females. Majority of them were found in the age of 14–30 years (52.5%) as compared to 31–60 years (34.5%) (Chi-square: 3219.463, p-value: 0.00). About 63% cases reported in low SES. Among the different categories of government employees affected with dengue, majority (4%) were belonging to health department (Chi-square: 4541.011, p-value: 0.00). Similarly, dengue targeted the dwellers living in multiple-storey houses (65%) as compared to those in the single-storeyed houses (35%) (Chi-square: 495.630, p-value: 0.00). The overall death toll observed was of 57 persons. Dengue prevailed more (38.4%) among low qualified individuals as compared to high qualified (11.5%) (Chi-square: 884.315, p-value: 0.00). Conclusion Our analysis indicated a decrease in the epidemiological trend of dengue (now) in the area, though initially it was observed affecting all types of communities on a larger scale. However, the DENV-2 and DENV-3 were dominantly circulating in the area and the prevalence (with usual peaks in post-monsoon) found high in males, illiterate (less educated) individuals and in those with low SES. Urbanization, infected human travelling, climate change, socioeconomic, sociodemographic as well as the wide range adaptation of vector mosquitoes, altogether, are the important factors playing role in the expansion of dengue. Further studies are needed to determine the association of these variables with the dengue spread in the area.
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Affiliation(s)
- Jehangir Khan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Sun Yat-sen University-Michigan State University Joint Center of Vector Control for Tropical Diseases, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Zoology, Abdul Wali Khan University Mardan (AWKUM), Khyber Pakhtunkhwa, Pakistan
- * E-mail:
| | - Abdul Ghaffar
- Department of Meteorology, COMSATS Institute of Information Technology Islamabad, Islamabad, Pakistan
| | - Shujaat Ali Khan
- Department of Biotechnology & Bioinformatics, Islamic International University Islamabad, Pakistan
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12
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Dias M, Pattabiraman C, Siddappa S, Gowda M, Shet A, Smith D, Muehlemann B, Tamma K, Solomon T, Jones T, Krishna S. Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum. Wellcome Open Res 2018; 3:44. [PMID: 30167467 PMCID: PMC6085601 DOI: 10.12688/wellcomeopenres.14438.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 08/17/2023] Open
Abstract
Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine. Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.
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Affiliation(s)
- Mary Dias
- St. John's Medical College and Hospital, Bangalore, 560034, India
| | - Chitra Pattabiraman
- National Institute of Mental Health and Neurosciences, India, Bangalore, 560029, India
| | - Shilpa Siddappa
- Centre for Cellular and Molecular Platforms, Bangalore, 560065, India
| | - Malali Gowda
- Trans-Disciplinary University, Foundation for Revitalization of Local Health Traditions, Bangalore, 560064, India
| | - Anita Shet
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Barbara Muehlemann
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | | | - Tom Solomon
- Institute of Infection and Global Health, and National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK
| | - Terry Jones
- Center for Pathogen Evolution, Department of
Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- World Health Organization
Collaborating Center for Modeling, Evolution, and Control of Emerging Infectious Diseases, Cambridge, CB2 3EJ, UK
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
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13
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Enam SF, Hashmi S. The importance of Evolutionary Medicine in developing countries: A case for Pakistan's medical schools. EVOLUTION MEDICINE AND PUBLIC HEALTH 2018; 2018:26-33. [PMID: 29492264 PMCID: PMC5822701 DOI: 10.1093/emph/eoy004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/21/2018] [Indexed: 01/16/2023]
Abstract
Evolutionary Medicine (EM) is a fundamental science exploring why our bodies are plagued with disease and hindered by limitations. EM views the body as an assortment of benefits, mistakes, and compromises molded over millennia. It highlights the role of evolution in numerous diseases encountered in community and family medicine clinics of developing countries. It enables us to ask informed questions and develop novel responses to global health problems. An understanding of the field is thus crucial for budding doctors, but its study is currently limited to a handful of medical schools in high-income countries. For the developing world, Pakistan's medical schools may be excellent starting posts as the country is beset with communicable and non-communicable diseases that are shaped by evolution. Remarkably, Pakistani medical students are open to studying and incorporating EM into their training. Understanding the principles of EM could empower them to tackle growing health problems in the country. Additionally, some difficulties that western medical schools face in integrating EM into their curriculum may not be a hindrance in Pakistan. We propose solutions for the remaining challenges, including obstinate religious sentiments. Herein, we make the case that incorporating EM is particularly important in developing countries such as Pakistan and that it is achievable in its medical student body.
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Affiliation(s)
- Syed Faaiz Enam
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Shumaila Hashmi
- Greater Manchester Mental Health Trust, Manchester M25 3BL, UK
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