Dataset on the epidemiology and genetic diversification of dengue virus (DENV) serotypes and genotypes in Mexico

Dengue virus (DENV) evolution has had a significant impact on disease pathogenesis, virulence, and epidemiology in Mexico. Novel genotypic variation in DENV serotypes and genotypes may influence the magnitude and severity of dengue epidemics, as evidenced by 2009 data from Veracruz State. The data presented herein is related to the publication entitled “Epidemiological Implications of the Genetic Diversification of Dengue Virus (DENV) Serotypes and Genotypes in Mexico” [1]. Raw data and trees provide epidemiological data on DENV prevalence and a comprehensive phylogeny of both representative sequences collected from an NCBI repository, and 28 additional isolates from acute-phase plasma samples diagnosed with dengue fever or severe dengue (Raw sequencing data is hosted in the public repository Mendeley Data (http://dx.doi.org/10.17632/bf2kdhhf6x.2). Phylogenetic trees for each DENV serotype (DENV-1, -2, -3 and -4) were constructed using these sequences by a maximum likelihood methodology as well as a Bayesian Markov chain Monte Carlo (MCMC) integration approach. Phylogenetic trees exhibited: (1) DENV-1, genotype V, (2) the DENV-2 Asian/American and Asian II genotypes, (3) DENV-3, genotype III, and (4) DENV-4, genotype I. This data can be beneficial for future analyses on DENV serotype and genotype structure and the introduction of novel DENV genotype sequences in the Americas, for the further elucidation of dengue etiology.

trees for each DENV serotype (DENV-1, -2, -3 and -4) were constructed using these sequences by a maximum likelihood methodology as well as a Bayesian Markov chain Monte Carlo (MCMC) integration approach. Phylogenetic trees exhibited: (1) DENV-1, genotype V, (2) the DENV-2 Asian/American and Asian II genotypes, (3) DENV-3, genotype III, and (4) DENV-4, genotype I. This data can be beneficial for future analyses on DENV serotype and genotype structure and the introduction of novel DENV genotype sequences in the Americas, for the further elucidation of dengue etiology.
© 2020 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license.

How data was acquired
Raw sequencing data is hosted in the public repository Mendeley Data ( http://dx.doi.org/10.17632/bf2kdhhf6x.2 ) [2] . This data was used to construct phylogenetic trees using divergence time (tMRCA) and rate of nucleotide substitution, built using a Bayesian Markov chain Monte Carlo (MCMC) integration approach, as implemented in BEAST 1.10.3 software [3] . A database of DENV representative sequences were collected freely from the NCBI repository: https://www.ncbi.nlm.nih.gov/genbank/ Raw DENV isolate data compiled freely from the GenBank database from both Veracruz State, and Mexico, as well as other countries, in addition to Mexican DENV epidemiological data from the Mexican SINAVE (Sistema Nacional de Vigilancia Epidemiologica de la Dirección General de Epidemiología/Epidemiological Surveillance Single Information System) ( Table 1 ) were acquired [4] . One Excel spreadsheet with pertinent raw data has been uploaded freely (Supplementary Table 1).

Data format
Raw sequencing data is hosted in the public repository Mendeley Data ( http://dx.doi.org/10.17632/bf2kdhhf6x.2 ) [2] . Data are in raw format and have been analyzed. Two tables have been uploaded, Table 1 and  Supplementary Table 1 (Excel spreadsheet).

Description of data collection
Epidemiological data of DENV ( Table 1 )

Value of the data
• This data will serve as a reference for future analyses on the incidence, epidemiology, and introduction of novel DENV genotypes/serotypes in Mexico-fostering a greater understanding of the emergence of variable dengue strains in the Americas. • All institutions involved in public health, disaster relief, and arbovirus control programs can benefit from this data through a more nuanced understanding of the association between specific genotypes (within serotypes) and presentation of disease. • Novel DENV sequence data from Mexico can aid the future phylogenetic classification of dengue serotypes and genotypes circulating in the Americas, useful to understanding virus evolution and the association between genotype/serotype and disease pathogenesis. • DNA sequencing and serotype identification of DENV samples in Veracruz State and elsewhere in Mexico can provide crucial supporting data for future control programs, reemergence research, source/sink studies, transnational transmission pattern analysis, and herd immunity research. • The epidemiological analysis of dengue virus in Veracruz State in 2009 can provide a foundation for further insight into the interrelationship between climatological factors, viral evolution, and disease distribution. Table 1 displays epidemiological data of DENV in both Mexico and Veracruz State specifically, between 1990 and 2019. Characteristics of the DENV sequences used to construct phylogenetic trees from Mexico and Veracruz State (GenBank accession number: EF5896 6 6 -EF5896 68 and MN711791 -MN711815) and additional representative sequences from the NCBI repository are presented in Supplementary Table 1, which also includes: GenBank accession number, URL: GenBank, strain or isolate, year collected, serotype, genotype, country, and ID in phylogenetic analyses. Alignment and sequences for DENV-1, -2, -3, and -4 are hosted in the public repository Mendeley Data ( http://dx.doi.org/10.17632/bf2kdhhf6x.2 ) [2] . Database details (Supplementary Table 1) includes: GenBank accession number, URL: GenBank, strain or isolate, year collected, serotype, genotype, country, ID in phylogenetic analyses, and references associated with each sequence. The phylogenetic trees for DENV-1, -2, -3, and -4 were constructed using the sequences of either the C-prM or NS3 gene regions. Fig. 1 displays the phylogeny of NS3 gene sequences for DENV-1. Sequences from Veracruz State were grouped within genotype V (labelled in bold), similar to other isolates from Latin America. The phylogeny of NS3 gene sequences for DENV-3 from both Veracruz and Oaxaca States (2009 and 2005 epidemics, respectively) presented as genotype III (labelled in bold; Fig. 2 ). The phylogenetic tree for DENV-2 illustrates isolates of the DENV-2 Asian/American genotype related to strains from Oaxaca ( Fig. 3 ). The DENV-2, Asian II genotype was shown to share a genetic affinity with dengue strains from Chilpancingo, and Acapulco, Mexico, as well as Colombia, Cuba, and China, both according to a maximum composite likelihood (MCL) methodology ( Fig. 3 ) and a Bayesian Markov chain Monte Carlo (MCMC) approach ( Fig. 4 ) [3] . The Bayesian trend moreover held true for Fig. 5 , where 384    . This phylogenetic tree includes five novel sequences clustered within the Asian/American genotype, and eleven novel sequences clustered within the Asian II genotype (labelled in bold). Positions of sequences from Mexico are indicated using a dot, and those from the Americas using a triangle. Horizontal branch lengths are proportional to the bar representing the probability of coalescence. DENV strains are named as follows: GenBank accession number/serotype/country/year/genotype.   instead of 134 nucleotides were used, omitting sequences of Guerrero State samples due to their relatively shorter length. DENV-4 isolates clustered with genotype I, sharing a recent common ancestor with strains from the Philippines and Brazil ( Fig. 6 ). Lastly, DENV-4 isolates, according to a Bayesian model, were found to cluster with isolates from China after omitting Brazilian sequences due to their inherently shorter length ( Fig. 7 ).

Epidemiology of dengue in Mexico
The data source of DEN incidence and number of cases in Mexico between 1990 and 2019 was the Mexican SINAVE [4] .

Sample collection
Sixty-five isolates of DENV viruses were obtained from acute-phase plasma collected from patients with dengue fever or severe dengue through the "Instituto Mexicano del Seguro Social"

Dengue virus isolation
Aedes albopictus clone C6/36 cells were grown in minimal essential media (MEM), supplemented with 10% fetal bovine serum (FBS) and nonessential amino acids. Cells were maintained at 28 °C without carbon dioxide (CO2). After 18 h of culture, cells (2 × 10 6 /100 mm plate) were infected with 0.2 ml DENV-2 inoculum with an input MOI of 600 PFU/cell and were incubated at 28 °C for 10 days.
Viruses were isolated as previously described [7] with a few modifications. After 18 hours of culture, C6/36 cells (2 × 10 6 /15 ml tube) were infected with 0.01 to 0.1 ml of serum specimen per tube, diluted to 1.0 ml with medium, and incubated for 2 h at 28 °C. After one wash, 3.0 ml of MEM was added, and cells were cultivated for approximately 15 days at 28 °C (passage number 1). Cells were observed daily and when a cytopathic effect was apparent from syncytium formation and cellular lysis, the cells were harvested and centrifuged at 3,0 0 0 rpm for 5 min. The pellet was then suspended in 0.6 ml of MEM and stored in aliquots of 0.15 ml at -70 °C. The supernatant (approximately 2.5 ml) was stored in 2 aliquots of 1.0 ml and one aliquot of 0.5 ml, at -70 °C. To obtain passage numbers two and three, C6/36 cells were incubated with 1.0 ml of the supernatant obtained from earlier passages, for 2 h at 28 °C following the same procedure as above. Serotypes in all samples were determined based on the isolates obtained from the first, second, or third culture passages.

RNA extraction
RNA was extracted from the cell culture supernatant using TRIzol TM LS reagent, Cat. No. 10296028 (Gibco, Gaithersburg, MD) according to the manufacturer's recommendations. Isopropanol-precipitated RNA was recovered by centrifugation, then air-dried. The resultant RNA pellet was suspended in 50 μl of diethyl pyrocarbonate (DEPC) treated water, Cat. No. 46-2224 (Invitrogen Life Technologies, Carlsbad, CA) and used as a template for reverse transcription with polymerase chain reaction (RT-PCR).

Ethics statement
This research project was reviewed and approved by the Institutional Review Board of the IMSS (Commission of Scientific Research) and the Bioethical Commission for Research in Humans of Center for Research and Advanced Studies of the National Polytechnic Institute (Comité de Bioética Para la Investigación en Seres Humanos, COBISH-CINVESTAV). Written informed consent was obtained from all patient.