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Whole genome analysis of dengue virus strains isolated in the Philippines was performed using an Illumina MiSeq next generation
sequencer and bioinformatics. Complete genome sequences of 24 DENV-2 isolated from 1995 to 2008 was mapped against a
DENV-2 reference sequence (NC_001474) from Genbank. The Philippine DENV-2 isolates were highly similar to strains from Taiwan
(AJ968413.1) and China (EF051521.1). The Chinese strain (EF051521.1) was isolated in 2001 yet similar strains could have been
circulating in the Philippines as early as 1998. The isolates highly similar to the Taiwanese strain were of the Asian II genotype and
the isolates highly similar to the Chinese strain were of the Cosmopolitan genotype. In total, 922 synonymous and non-synonymous
substitutions were observed, of which 232 (25.2%) were in the NS5 gene, which had the most substitutions. This was followed by NS3
with 181 (19.6%) and the E gene with 144 (15.6%) and the 2K gene with only 6 (0.7%). Putative amino acid sequences from the coding
regions revealed that majority (817, 88.6%) of the substitutions were synonymous or silent. Of the remaining 105 non-synonymous
mutations, 22 (20.9%) were in the NS5 gene followed by the NS1 and E genes with 20 (19.0%) and 16 (15.2), respectively. When the
clustered genetic variation profiles were identified based on the specific clinical diagnosis, all the DHF III cases belonged to a single
cluster together with some DF cases and one SVI case. In contrast, all DHF I-II and most of the DF cases grouped together in another
cluster. All DHF III cases were of the Cosmopolitan genotype. DENV circulating within the Philippines from 1995 to 1998 were of the
Asian genotype, followed by a period from 1998 to 2001 in which both the Asian II and Cosmopolitan strains co-circulated and from
2000 to 2008 the circulating DENV was primarily cosmopolitan. This supports previous observations of a probable genotype shift in
the Philippines. This is the first report of whole genome analyses of dengue virus isolates from the Philippines.
Maria Luisa G Daroy is a Scientist at the Research and Biotechnology Division of St. Luke’s Medical Center and Assistant Professor in the MS Molecular Medicine Program of the St. Luke’s College of Medicine-WHQ Memorial. She has published more than 20 papers on dengue, Japanese encephalitis, chikungunya, eye infections, dementia, diabetes and coronary artery disease. She was the Chair of the Board of Examiners of the Philippine Academy for Microbiology from 2013-2015 and authored a book chapter on Philippine microbiology research. Researches include dengue, chikungunya, diarrhea, CNS infections, pathogen genomics, antimicrobial resistance, plant antivirals, molecular diagnostics and genetics of CVD, thyroid cancer and dementia.