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genotyping dengue 2

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https://www.readbyqxmd.com/read/28600724/phylogenetic-and-evolutionary-analyses-of-dengue-viruses-isolated-in-jakarta-indonesia
#1
C S Whinie Lestari, Benediktus Yohan, Anisa Yunita, Febrina Meutiawati, Rahma Fitri Hayati, Hidayat Trimarsanto, R Tedjo Sasmono
Dengue has affected Indonesia for the last five decades and become a major health problem in many cities in the country. Jakarta, the capital of Indonesia, reports dengue cases annually, with several outbreaks documented. To gain information on the dynamic and evolutionary history of dengue virus (DENV) in Jakarta, we conducted phylogenetic and evolutionary analyses of DENV isolated in 2009. Three hundred thirty-three dengue-suspected patients were recruited. Our data revealed that dengue predominantly affected young adults, and the majority of cases were due to secondary infection...
June 9, 2017: Virus Genes
https://www.readbyqxmd.com/read/28599625/genetic-variants-of-micb-and-plce1-and-associations-with-the-laboratory-features-of-dengue
#2
James Whitehorn, Duong Thi Hue Kien, Nguyen Than Ha Quyen, Bridget Wills, Nguyen Van Vinh Chau, Dong Thi Hoai Tam, Nguyen Minh Tuan, Thomas Jaenisch, Martin Hibberd, Chiea Chuen Khor, Cameron P Simmons
BACKGROUND: A previous genome-wide association study identified 2 susceptibility loci for severe dengue at MICB rs3132468 and PLCE1 rs3740360 and further work showed these mutations to be also associated with less severe clinical presentations. The aim of this study was to determine if these specific loci were associated with laboratory features of dengue that correlate with clinical severity with the aim of elucidating the functional basis of these genetic variants. METHODS: This was a case-only analysis of laboratory-confirmed dengue patients obtained from 2 prospective cohort studies and 1 randomised clinical trial in Vietnam (Trial registration: ISRCTN ISRCTN03147572...
June 9, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28575000/clinical-and-virological-characteristics-of-dengue-in-surabaya-indonesia
#3
Puspa Wardhani, Aryati Aryati, Benediktus Yohan, Hidayat Trimarsanto, Tri Y Setianingsih, Dwiyanti Puspitasari, Muhammad Vitanata Arfijanto, Bramantono Bramantono, Suharto Suharto, R Tedjo Sasmono
Dengue disease is still a major health problem in Indonesia. Surabaya, the second largest city in the country, is endemic for dengue. We report here on dengue disease in Surabaya, investigating the clinical manifestations, the distribution of dengue virus (DENV) serotypes, and the relationships between clinical manifestations and the genetic characteristics of DENV. A total of 148 patients suspected of having dengue were recruited during February-August 2012. One hundred one (68%) of them were children, and 47 (32%) were adults...
2017: PloS One
https://www.readbyqxmd.com/read/28544099/genetic-signatures-coupled-with-lineage-shift-characterize-endemic-evolution-of-dengue-virus-serotype-2-during-2015-outbreak-in-delhi-india
#4
Manish Chandra Choudhary, Ekta Gupta, Shvetank Sharma, Nadeem Hasnain, Pragya Agarwala
OBJECTIVE: In 2015 New Delhi witnessed a massive outbreak of Dengue virus (DENV) resulting in high morbidity and mortality. We report the molecular characterization of the dominant circulating DENV strain to understand its evolution and dispersal. MATERIALS AND METHODS: DENV infections were diagnosed by detection of IgM/NS1 antigen and serotyping was performed by C-PrM PCR. Envelope gene was amplified and variation(s) in envelope gene were analyzed. Phylogenetic tree construction, time-based phylogeny and origin of DENV were analyzed...
May 23, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28531223/dengue-in-bali-clinical-characteristics-and-genetic-diversity-of-circulating-dengue-viruses
#5
Dewi Megawati, Sri Masyeni, Benediktus Yohan, Asri Lestarini, Rahma F Hayati, Febrina Meutiawati, Ketut Suryana, Tangking Widarsa, Dewa G Budiyasa, Ngurah Budiyasa, Khin S A Myint, R Tedjo Sasmono
A high number of dengue cases are reported annually in Bali. Despite the endemicity, limited data on dengue is available for Bali localities. Molecular surveillance study was conducted to explore the clinical and virological characteristics of dengue patients in urban Denpasar and rural Gianyar areas in Bali during the peak season in 2015. A total of 205 adult dengue-suspected patients were recruited in a prospective cross-sectional study. Demographic and clinical information were obtained, and dengue screening was performed using NS1 and IgM/IgG ELISAs...
May 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28482813/epidemiological-and-molecular-characteristics-of-emergent-dengue-virus-in-yunnan-province-near-the-china-myanmar-laos-border-2013-2015
#6
Ting-Song Hu, Hai-Lin Zhang, Yun Feng, Jian-Hua Fan, Tian Tang, Yong-Hua Liu, Liu Zhang, Xiao-Xiong Yin, Gang Chen, Hua-Chang Li, Jin Zu, Hong-Bin Li, Yuan-Yuan Li, Jing Yu, Fu-Qiang Zhang, Quan-Shui Fan
BACKGROUND: Yunnan Province is located in southwestern China and neighbors the Southeast Asian countries, all of which are dengue-endemic areas. In 2000-2013, sporadic imported cases of dengue fever (DF) were reported almost annually in Yunnan Province. During 2013-2015, we confirmed that a large-scale indigenous DF outbreak emerged in cities of Yunnan Province near the China-Myanmar-Laos border. METHODS: Epidemiological characteristics of DF in Yunnan Province during 2013-2015 were evaluated by retrospective analysis...
May 8, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28456663/comparative-whole-genome-analysis-of-dengue-virus-serotype-2-strains-differing-in-trans-endothelial-cell-leakage-induction-in-vitro
#7
Sneha Singh, M G Anupriya, Easwaran Sreekumar
The role of genetic differences among dengue virus (DENV) in causing increased microvascular permeability is less explored. In the present study, we compared two closely related DENV serotype-2 strains of Cosmopolitan genotype for their in vitro infectivity phenotype and ability to induce trans-endothelial leakage. We found that these laboratory strains differed significantly in infecting human microvascular endothelial cells (HMEC-1) and hepatocytes (Huh7), two major target cells of DENV in in vivo infections...
April 27, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28450505/complete-coding-sequences-of-two-dengue-virus-type-2-strains-isolated-from-an-outbreak-in-burkina-faso-in-2016
#8
Cécile Baronti, Géraldine Piorkowski, Franck Touret, Rémi Charrel, Xavier de Lamballerie, Antoine Nougairede
We report here the complete coding sequences of two strains of dengue virus type 2, isolated in France from patients returning from Burkina Faso in November 2016. Both strains (cosmopolitan genotype) are almost identical (99.91% nucleotide identity) and closely related to a strain circulating in Burkina Faso in 1983.
April 27, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28388922/viral-and-serological-kinetics-in-zika-virus-infected-patients-in-south-korea
#9
Young Eui Jeong, Go-Woon Cha, Jung Eun Cho, Eun Ju Lee, Youngmee Jee, Won-Ja Lee
Zika virus is a mosquito-borne flavivirus that causes clinical symptoms similar to those observed in dengue and chikungunya virus infections. The Korea Centers for Disease Control and Prevention initiated laboratory testing using a real-time reverse transcription-polymerase chain reaction in January 2016. More than 1,000 suspected cases of infection were tested and nine were confirmed as imported cases of Zika virus infection from January to July 2016. The travel destinations of the infected individuals were Brazil, Philippines, Viet Nam, Guatemala, Puerto Rico, and the Dominican Republic...
April 7, 2017: Virology Journal
https://www.readbyqxmd.com/read/28367875/laboratory-and-molecular-characterization-of-dengue-virus-during-the-2014-outbreak-in-guangfo-region-southern-china
#10
Zhao-Fan Luo, Bo Hu, Feng-Yi Zhang, Xiang-Hua Lin, Xiao-Ying Xie, Kun-Yi Pan, Hong-Yu Li, Rui-Wen Ren, Wen-Zhong Zhao
Non-specific symptoms and low viremia levels make early diagnosis of dengue virus (DENV) infection challenging. This study aimed to 1) identify laboratory markers which can predict a positive laboratory diagnosis, and 2) perform a molecular characterization of DENV from the 2014 Guangdong epidemic. This retrospective study enrolled 1044 patients from the Guangdong epidemic who had clinically suspected dengue. Viral RNA was detected by real-time RT-PCR and viral-specific NS1 antigen was detected using ELISA...
March 28, 2017: Japanese Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28241052/osbpl10-rxra-and-lipid-metabolism-confer-african-ancestry-protection-against-dengue-haemorrhagic-fever-in-admixed-cubans
#11
Beatriz Sierra, Petr Triska, Pedro Soares, Gissel Garcia, Ana B Perez, Eglys Aguirre, Marisa Oliveira, Bruno Cavadas, Béatrice Regnault, Mayling Alvarez, Didye Ruiz, David C Samuels, Anavaj Sakuntabhai, Luisa Pereira, Maria G Guzman
Ethnic groups can display differential genetic susceptibility to infectious diseases. The arthropod-born viral dengue disease is one such disease, with empirical and limited genetic evidence showing that African ancestry may be protective against the haemorrhagic phenotype. Global ancestry analysis based on high-throughput genotyping in admixed populations can be used to test this hypothesis, while admixture mapping can map candidate protective genes. A Cuban dengue fever cohort was genotyped using a 2.5 million SNP chip...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28120220/molecular-epidemiology-demonstrates-that-imported-and-local-strains-circulated-during-the-2014-dengue-outbreak-in-guangzhou-china
#12
Geng Li, Pan Pan, Qiuyan He, Xiujuan Kong, Kailang Wu, Wei Zhang, Yuntao Liu, Huiting Huang, Jianbo Liu, Zhongde Zhang, De Wu, Xiaoping Lai, Xiaohong Liu, Jianguo Wu
The dengue virus (DENV) is a vital global public health issue. The 2014 dengue epidemic in Guangzhou, China, caused approximately 40,000 cases of infection and five deaths. We carried out a comprehensive investigation aimed at identifying the transmission sources in this dengue epidemic. To analyze the phylogenetics of the 2014 dengue strains, the envelope (E) gene sequences from 17 viral strains isolated from 168 dengue patient serum samples were sequenced and a phylogenetic tree was reconstructed. All 17 strains were serotype I strains, including 8 genotype I and 9 genotype V strains...
February 2017: Virologica Sinica
https://www.readbyqxmd.com/read/28100385/-phylogenetic-analysis-of-envelope-gene-of-dengue-virus-serotype-2-in-guangzhou-2001-2015
#13
Y Liu, L Y Jiang, L Luo, Y M Cao, Q L Jing, Z C Yang
Objective: To investigate the molecular characteristics of dengue virus serotype 2 (DENV2) in Guangzhou during 2001-2015, and analyze the E gene of the strains isolated, the phylogenetic tree and molecular clock were constructed to know about the evolution of the strains. Methods: The serum samples of the patients were detected by real time PCR, and positive samples were used to isolate dengue virus by using C6/36 cells. The E gene of the isolated strains were sequenced. The phylogenetic tree was constructed by using software Mega 4...
January 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28004020/molecular-epidemiology-and-evolutionary-analysis-of-dengue-virus-type-2-circulating-in-delhi-india
#14
Pankaj Sharma, Veena Mittal, Mala Chhabra, Roop Kumari, Priyanka Singh, Srinivas Venkatesh
Dengue virus type 2 (DENV-2) has been associated with severe dengue outbreaks in many countries including India. Its predominance was recorded nearly after a decade in the capital city, Delhi in 2013. The present study characterizes DENV-2 circulated during 2013-2014. Analysis based on envelope (E) gene showed the presence of two clades (I and II) of DENV-2, within the Cosmopolitan genotype. Analysis of time of most recent common ancestor revealed the existence of clade I for more than a decade (95 % HPD 13-16 years) however, clade II showed comparatively recent emergence (95 % HPD 5-13 years)...
December 2016: Virusdisease
https://www.readbyqxmd.com/read/27983492/meningitis-associated-with-simultaneous-infection-by-multiple-dengue-virus-serotypes-in-children-brazil
#15
Paula Eillanny Silva Marinho, Danilo Bretas de Oliveira, Talitah Michel Sanchez Candiani, Ana Paula Correia Crispim, Pedro Paulo Martins Alvarenga, Fabrizia Cristina Dos Santos Castro, Jonatas Santos Abrahão, Maria Rios, Roney Santos Coimbra, Erna Geessien Kroon
To determine the causes of viral meningitis, we analyzed 22 cerebrospinal fluid samples collected during the 2014-2015 dengue epidemics in Brazil. We identified 3 serotypes of dengue virus (DENV-1, -2, and -3), as well as co-infection with 2 or 3 serotypes. We also detected the Asian II genotype of DENV-2.
January 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/27982730/meta-analysis-of-the-relationship-between-tnf-%C3%AE-308g-a-and-il-10-819c-t-gene-polymorphisms-and-susceptibility-to-dengue
#16
Ana Caroline Melo Dos Santos, Edilson Leite de Moura, Jean Moisés Ferreira, Barbara Rayssa Correia Dos Santos, Verônica de Medeiros Alves, Karol Fireman de Farias, Elaine Virgínia Martins de Souza Figueiredo
OBJECTIVE: This study determined whether tumor necrosis factor alpha (TNF-α) and Interleukin-10 (IL-10) polymorphisms are associated with susceptibility to dengue. METHODS: a systematic review with meta-analysis was conducted of the associations between the TNF-α (-308G/A) and IL-10 (-819C/T) polymorphisms and dengue. RESULTS: A total of eight case-controls studies involving 384 individuals with symptomatic dengue, 571 individuals with dengue hemorrhagic fever, and 995 healthy controls were considered in the meta-analysis...
February 2017: Immunological Investigations
https://www.readbyqxmd.com/read/27902331/the-plasma-virome-of-febrile-adult-kenyans-shows-frequent-parvovirus-b19-infections-and-a-novel-arbovirus-kadipiro-virus
#17
Carolyne N Ngoi, Juliana Siqueira, Linlin Li, Xutao Deng, Peter Mugo, Susan M Graham, Matt A Price, Eduard J Sanders, Eric Delwart
Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75 %), pegivirus C (GBV-C) (67 %), alpha anellovirus (59 %), gamma anellovirus (55 %), beta anellovirus (41 %), dengue virus genotype 2 (DENV-2) (16 %), human immunodeficiency virus type 1 (6 %), human herpesvirus 6 (6 %), HBV (4 %), rotavirus (4 %), hepatitis B virus (4 %), rhinovirus C (2 %), Merkel cell polyomavirus (MCPyV; 2 %) and Kadipiro virus (2 %)...
December 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27765124/-study-of-epidemiological-characteristics-and-viral-sources-of-dengue-fever-outbreak-in-guangxi-zhuang-autonomous-region-2014
#18
M M Chen, Y Tan, Z Z Tang, M Lin, K J Zhou, W T He, Y P Yang, J Wang
Objective: To understand the epidemiological characteristics and viral sources of dengue fever outbreak in Guangxi Zhuang Autonomous Region (Guangxi) in 2014. Methods: A combined analysis of epidemiological characteristics and genetic characteristics were performed in this study. The time, population and area distributions of the cases were analyzed. Serum samples were collected from dengue fever cases to detect NS1 antigen by using commercial ELISA kits according to the guideline of the manufacture. RT-PCR assay was conducted to detect dengue virus in NS1 positive samples...
October 10, 2016: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/27722053/epidemiological-and-molecular-characterization-of-dengue-viruses-imported-into-guangzhou-during-2009-2013
#19
Yongxia Shi, Shufen Li, Xiaobo Li, Kui Zheng, Shuai Yuan, Jicheng Huang
BACKGROUND: Dengue virus causes one of the most significant infectious diseases in tropical and subtropical regions, notable number of which is imported into China every year. RESULTS: In this study, the molecular epidemiologic and phylogenetic analyses of dengue cases imported into Guangzhou in South China during 2009-2013 were conducted. During that period, 46 imported dengue cases were identified, including four serotypes. Most of the dengue patients were travelling from Southeast Asia, South Asia and Africa...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27681163/molecular-characterization-and-viral-origin-of-the-2015-dengue-outbreak-in-xishuangbanna-yunnan-china
#20
Yujiao Zhao, Lihua Li, Dehong Ma, Jia Luo, Zhiqiang Ma, Xiaodan Wang, Yue Pan, Junying Chen, Juemin Xi, Jiajia Yang, Lijuan Qiu, Chunhai Bai, Liming Jiang, Xiyun Shan, Qiangming Sun
A total of 1067 serum samples were collected from febrile patients in Xishuangbanna, Yunnan, 2015. Of these, 852 cases were confirmed to be dengue NS1-positive. 76 structural protein genes were sequenced through RT-PCR based on the viral RNAs extracted from serum samples. Phylogenetic analysis revealed that all strains were classified as cosmopolitan genotype of DENV-2. After comparing with the DENV-2SS, 173 base substitutions were found in 76 sequences, resulting in 43 nonsynonymous mutations, of which 22 mutations existed among all samples...
September 29, 2016: Scientific Reports
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