Efficiency comparison of four high-fidelity DNA polymerases for dengue virus detection and genotype identification in field-caught mosquitoes

Agriculture and Natural Resources - Tập 52 - Trang 84-92 - 2018
Thikhumporn Sittivicharpinyo1, Passorn Wonnapinij1,2, Wunrada Surat1,2
1Evolutionary Genetics and Computer Biology Research Unit, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Lat Yao District, Chatuchak, Bangkok 10900, Thailand
2Centre for Advanced Studies in Tropical Natural Resources, National Research, University-Kasetsart University (CASTNAR, NRU-KU, Thailand), 50 Ngam Wong Wan, Road, Lat Yao District, Chatuchak, Bangkok, 10900, Thailand

Tài liệu tham khảo

Ahmed, 2014, Comparison of NS1 antigen detection ELISA, real time RT-PCR and virus isolation for rapid diagnosis of dengue infection in acute phase, J. Vector Borne Dis., 51, 194 Alfonso, 2012, Phylogenetic relationship of dengue virus type 3 isolated in Brazil and Paraguay and global evolutionary divergence dynamics, Virol. J., 9, 124, 10.1186/1743-422X-9-124 Añez, 2011, Circulation of different lineages of dengue virus type 2 in Central America, their evolutionary time-scale and selection pressure analysis, PLoS One, 6, e27459, 10.1371/journal.pone.0027459 Arezi, 2003, Amplification efficiency of thermostable DNA polymerases, Anal. Biochem., 321, 226, 10.1016/S0003-2697(03)00465-2 Das, 2008, Detection and serotyping of dengue virus in serum samples by multiplex reverse transcriptase PCR-ligase detection reaction assay, J. Clin. Microbiol., 46, 3276, 10.1128/JCM.00163-08 Domingo, 2011, Molecular surveillance of circulating dengue genotypes through European travelers, J. Trav. Med., 18, 183, 10.1111/j.1708-8305.2011.00501.x Domingo, 2006, Use of a short fragment of the C-terminal E gene for detection and characterization of two new lineages of dengue virus 1 in India, J. Clin. Microbiol., 44, 1519, 10.1128/JCM.44.4.1519-1529.2006 Drumond, 2013, Circulation of different lineages of Dengue virus 2, genotype American/Asian in Brazil, dynamics and molecular and phylogenetic characterization, PLoS One, 8, e59422, 10.1371/journal.pone.0059422 Fatima, 2011, Serotype and genotype analysis of dengue virus by sequencing followed by phylogenetic analysis using samples from three mini outbreaks-2007-2009 in Pakistan, BMC Microbiol., 11, 200, 10.1186/1471-2180-11-200 Fried, 2010, Serotype-specific differences in the risk of dengue hemorrhagic fever, an analysis of data collected in Bangkok, Thailand from 1994 to 2006, PLoS Neglected Trop. Dis., 4, e617, 10.1371/journal.pntd.0000617 Huang, 2014, A pictorial key to the species of Aedes (Ochlerotatus and Coetzeemyia) in the Afrotropical region (Diptera, Culicidae), Zootaxa, 3754, 592, 10.11646/zootaxa.3754.5.5 Idrees, 2012, A brief review on dengue molecular virology, diagnosis, treatment and prevalence in Pakistan, Genet. Vaccine Ther., 10, 6, 10.1186/1479-0556-10-6 Jarman, 2008, Microevolution of dengue viruses circulating among primary school children in Kamphaeng Phet, Thailand. J. Virol, 82, 5494, 10.1128/JVI.02728-07 Jittmittraphap, 2006, Rapid detection of dengue viral RNA in mosquitoes by nucleic acid-sequence based amplification (NASBA), Southeast Asian J. Trop. Med. Publ. Health, 37, 1117 Ketkaew, 2016 Khawsak, 2003, Determination of dengue virus serotypes in Thailand using PCR based method, Southeast Asian J. Trop. Med. Publ. Health, 34, 781 Klungthong, 2008, Molecular genotyping of dengue viruses by phylogenetic analysis of the sequences of individual genes, J. Virol. Meth., 154, 175, 10.1016/j.jviromet.2008.07.021 Klungthong, 2004, The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand, Virology, 329, 168, 10.1016/j.virol.2004.08.003 Kumaria, 2010, Correlation of disease spectrum among four dengue serotypes, a five years hospital based study from India, Braz. J. Infect. Dis., 14, 141, 10.1016/S1413-8670(10)70027-1 Kuno, 1998, Phylogeny of the genus Flavivirus, J. Virol., 72, 73, 10.1128/JVI.72.1.73-83.1998 Lanciotti, 1992, Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction, J. Clin. Microbiol., 30, 545, 10.1128/JCM.30.3.545-551.1992 Lee, 2012, Dengue virus surveillance in Singapore reveals high viral diversity through multiple introductions and in situ evolution, Infect. Genet. Evol., 12, 77, 10.1016/j.meegid.2011.10.012 Lequime, 2016, Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes, PLoS Genet., 12, 10.1371/journal.pgen.1006111 Maneekan, 2009, Development of single-tube mutiplex RT-PCR for dengue virus typing, Southeast Asian J. Trop. Med. Publ. Health, 40, 1254 Miura, 2013, Comparison of six commercially-available DNA polymerases for direct PCR, Rev. Inst. Med. Trop. Sao Paulo, 55, 401, 10.1590/S0036-46652013000600005 Najioullah, 2014, Evaluation of four commercial real-time RT-PCR kits for the detection of dengue viruses in clinical samples, Virol. J., 11, 164, 10.1186/1743-422X-11-164 Nilsson, 2016, Comparison of DNA polymerases for improved forensic analysis of challenging samples, Forensic Sci. Int. Genet., 24, 55, 10.1016/j.fsigen.2016.05.017 Nisalak, 2003, Serotype-specific dengue virus circulation and dengue disease in Bangkok, Thailand from 1973 to 1999, Am. J. Trop. Med. Hyg., 68, 191, 10.4269/ajtmh.2003.68.191 Pan, 2007, The structure of a birnavirus polymerase reveals a distinct active site topology, Proc. Natl. Acad. Sci. U.S.A., 104, 7385, 10.1073/pnas.0611599104 Peeling, 2010, Evaluation of diagnostic tests, dengue, Nat. Rev. Microbiol., 8, S30, 10.1038/nrmicro2459 Peña-García, 2016, Infection rates by dengue virus in mosquitoes and the influence of temperature may be related to different endemicity patterns in three Colombian cities, Int. J. Environ. Res. Publ. Health, 13, 734, 10.3390/ijerph13070734 Poloni, 2010, Detection of dengue virus in saliva and urine by real time RT-PCR, Virol. J., 7, 22, 10.1186/1743-422X-7-22 Purzycka, 2006, Efficiency comparison of seven different Taq polymerases used in hemogenetics, 719 R Development Core Team R, 2013 Rico-Hesse, 2003, Microevolution and virulence of dengue viruses, Adv. Virus Res., 59, 315, 10.1016/S0065-3527(03)59009-1 Rico-Hesse, 2010, Dengue virus virulence and transmission determinants, 45 Teoh, 2015, Early detection of dengue virus by use of reverse transcription-recombinase polymerase amplification, J. Clin. Microbiol., 53, 830, 10.1128/JCM.02648-14 Vicente, 2016, 16, 320 World Health Organization, 2016 Yung, 2015, Dengue serotype-specific differences in clinical manifestation, laboratory parameters and risk of severe disease in adults, Singapore, Am. J. Trop. Med. Hyg., 92, 999, 10.4269/ajtmh.14-0628