Genome sequence of a vesicular stomatitis Indiana virus isolate collected in 1988 from a naturally infected bovine in Mexico

ABSTRACT

We report the near-full genome sequence of a vesicular stomatitis Indiana virus (VSIV) originally collected from a naturally infected bovine in south-central Mexico. This sequence represents a coding-complete genome sequence of a VSIV from Mexico, a country where vesicular stomatitis is endemic.

ANNOUNCEMENT

Vesicular stomatitis virus (VSV) (order Mononegavirales, family Rhabdoviridae, and genus Vesiculovirus) causes vesicular lesions on or around the mouth, udders, and coronary bands of cattle, pigs, and horses (1). It has two main serotypes, vesicular stomatitis Indiana virus (VSIV) and vesicular stomatitis New Jersey virus (VSNJV), and is considered endemic from southern Mexico to northern South America with outbreaks occurring in the United States every ~5–10 years (2–4). The endemic region of Mexico contains a range of genetically diverse lineages of VSV concurrently circulating, and phylogenetic analysis indicates that some of these lineages may become the precursors of the lineages causing intermittent outbreaks in the United States (5). Here we report the coding-complete genome sequence of a VSIV isolate from Mexico. To the authors’ knowledge, this is the first VSIV coding-complete genome sequence from Mexico in a public database.

In 1988, a field sample (unspecified) was taken from a naturally infected bovine in Morelos, Mexico, and kept frozen at −70°C until it was passaged four times in Vero cells (6) before a final intradermalingual passage in a steer in 1994. A 1:50 suspension of tongue tissue in MEM with antibiotics was successively filtered through 0.8 and 0.2 µm filters before storage at −70°C. In 2023, at the Plum Island Animal Disease Center, total nucleic acid was extracted from the 0.2 µm filtrate and sequenced as previously described (7). Briefly, the MagMax Pathogen RNA/DNA extraction kit (Applied Biosystems) was used on a Kingfisher Flex platform (Thermo Scientific). First-strand cDNA synthesis was performed using SuperScript III RT (Invitrogen) and tagged random and oligo dT primers, second-strand synthesis was performed with Sequenase (Affymetrix) and the dsDNA was amplified with TaKaRa Taq Version 2.0 (TakaraBio) (7). A sequencing library was constructed with the Nextera XT kit (Illumina) and sequenced with a paired-end 500-cycle MiSeq Reagent Kit v2 on an Illumina MiSeq platform. Bioinformatic analyses were performed in CLC Genomics Workbench (Qiagen) v21.0.4 using default parameters. Reads were trimmed for quality and then mapped to the reference sequence IN98COE (AF473864.1). Of the 8,710,395 total reads, 805,305 reads (Table 1) with an average length of 209.49 nt aligned to the reference, yielding average and median depths of coverage of 9223.4 and 5156.0, respectively. A consensus sequence was extracted from all nucleotide positions with a coverage depth of ≥10 reads.

TABLE 1.

NGS metrics obtained from the Illumina MiSeq

Isolate	Location	Date of collection	Infected species	# of VSIV reads	Avg. read length after quality trim	Total # of reads	Avg. coverage (fold)	GC content (%)	GenBank accession #	SRA accession #
IN88MRB	Morelos, Mexico	1988	Bos taurus	805,305	209.49	8,710,395	9223.4	41.60	OR921183	PRJNA1049804

While the exact genomic termini were not experimentally determined, an 11,161 nt coding-complete genome with a GC content of 41.56% was deduced. This isolate had the same genomic organization observed in other field isolates of VSIV. The closest BLASTn match (8) for the coding-complete genome is a recombinant derivative of the laboratory-adapted Mudd-Summers strain (AM690336.1) with 97.97% identity. The closest BLASTn match for the P gene (the gene most commonly used for phylogenetic analysis (9) is a field isolate from the Federal District of Mexico collected in 1986 (M35215.1) with 99.61% identity. This coding-complete genome sequence of a VSIV from Mexico should be useful for diagnostic assays and studies exploring VSIV virulence and epidemiology.

DATA AVAILABILITY

The coding-complete genome consensus sequence of IN88MRB described herein has been deposited in GenBank under accession no. OR921183. The raw data used to generate these consensus sequences are available in the Sequence Read Archive under no. SRX22811974, BioProject PRJNA1049804.