We succeeded in obtaining 28 complete coding sequences from 40 patients with DENV1 infection with more than 30 coverage. All of the newly identified DENV1 sequences from northern Vietnam fell into the genotype I cluster, which is dominant in southeastern and eastern Asia (Fig. 1a). This cluster could be separated into four subclusters and was close to the JQ045660 isolate obtained in Vietnam in 2011. Notably, these isolates were phylogenetically distinct from the strains identified in China during the same period (MF681693, MF683116, and MF681692) , suggesting that the origin of DENV1 in northern Vietnam was different from the isolates found in nearby areas. We identified 135 amino acid substitutions in comparison with the standard genotype 1 strain, EU848545, and nine substitutions were conserved in all newly sequenced samples. Two substitutions are in the structural region, A173T in precursor membrane (PrM), and V312L in the Envelope protein (E). Seven of these substitutions were in the nonstructural region, including one in the Nonstructural protein 1 (NS1) (H111Y), one in NS2A (K218R), one in NS4B (T27A), and four in NS5 (R378K, K551R, V787I, and E833G) (Additional file 1: Table S1).
Available full-length genome sequences of DENV1 are insufficient for detailed analyses, therefore we analyzed the E gene region (approximately 1483 bp) together with reference sequences obtained from the Virus Pathogen Database and Analysis Resource (ViPR, NCBI) before the year of 2017 . In total, we analyzed 1215 sequences from isolates obtained from southeastern and eastern Asia (287 from China, 261 from Thailand, 98 from Cambodia, 90 from Laos, 132 from Myanmar, 75 from Malaysia, and 272 from Vietnam; Additional file 2: Table S2). We aligned all the sequences using MEGA7 and then constructed a phylogenetic tree using the maximum likelihood (ML) method with 100 bootstraps . Consistent with the whole genome analysis results, the 2017 Northern Vietnamese sequences fell into a single cluster with four closely related subgroups (Fig. 1b). The cluster included Vietnam isolates obtained in 2008 and 2016, in addition to two sequences from China (2012 and 2014), and one from Cambodia (2013). Chinese isolates in 2017 formed a distinct cluster with other Chinese, Malaysian, and Vietnamese isolates, which suggested that the group of DENV1 causing the large-scale outbreak in 2017 was circulating locally in the area. The cluster containing 2017 isolates encoded the V312L substitutions in the E region. On the database, the V312L substitution did not find any other group of DENV1.
The analysis of IgM and IgG indicated that 13 samples were categorized as a primary infection, and 13 samples as secondary infection (2 samples were not available because of the small sample volume) (Additional file 3: Table S3). For the phylogenetical analysis and amino acid sequence comparison, we did not observe conserved substitutions according to the infection status.
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