First Genome Sequence of Foot-and-Mouth Disease Virus Serotype O Sublineage Ind2001e from Southern Vietnam

We report the polyprotein coding sequence of the newly defined Ind2001e sublineage of foot-and-mouth disease virus (FMDV) serotype O, isolated from a bovine epithelial tissue sample collected in 2017 in Kon Tum Province, Vietnam. This discovery updates FMDV diversity in Vietnam, has implications for FMDV epidemiology, and influences future vaccine selections.

ABSTRACT

We report the polyprotein coding sequence of the newly defined Ind2001e sublineage of foot-and-mouth disease virus (FMDV) serotype O, isolated from a bovine epithelial tissue sample collected in 2017 in Kon Tum Province, Vietnam. This discovery updates FMDV diversity in Vietnam, has implications for FMDV epidemiology, and influences future vaccine selections.

ANNOUNCEMENT

Foot-and-mouth disease (FMD) virus (FMDV; Apthovirus, Picornaviridae) is the etiologic agent of FMD, which is one of the most economically impactful infectious diseases globally. Acutely infected animals develop characteristic vesicles, most notably on the feet and in oral cavities (1). The seven distinct FMDV serotypes (A, Asia1, C, O, and SAT1 through SAT3) are defined based on VP1 sequences (2). In 2001, a distinct lineage of FMDV serotype O emerged in India (Ind2001), phylogenetically grouping in the Middle East-South Asia (ME-SA) topotype that diverged into sublineages a through d between 2001 and 2016 (3, 4). In 2017, a novel sublineage, designated O/ME-SA/Ind2001e, was detected in Bhutan, Sri Lanka, and Vietnam (5–7).

The virus described herein, O/VIT/8338/2017, was isolated from bovine epithelial tissue collected in Kon Tum Province, Vietnam, in April 2017. The sample tested positive for FMDV by virus isolation (VI) on LFBK-α_vβ₆ cells and was further confirmed by FMDV-specific real-time reverse transcription (rRT)-PCR. Total cell supernatant RNA was deep sequenced similarly to previously described methods (8). In brief, RNA was extracted using the MagMAX total RNA isolation kit, and genomic DNA was depleted from total RNA using a DNA-free DNase kit (Ambion) as specified by the manufacturer. Treated RNA underwent first-strand synthesis using the Superscript II first-strand synthesis system (Invitrogen) with random primers and two FMDV-specific primers located in the 3′ and 5′ regions (one each). Double-stranded cDNA was generated using an NEBNext Ultra nondirectional RNA second-strand synthesis module and purified with SPRIselect beads. The purified cDNA was prepped for deep sequencing using the Nextera XT kit on a NextSeq platform. The NextSeq run generated 36,278,126 total reads, which were trimmed for quality, resulting in an average read length of 148 nucleotides (nt). Within individual samples, reads were de novo assembled and contigs were annotated based on comparison with the closest BLASTn sequences. In the specified sample, 4,858 reads generated a de novo FMDV polyprotein contig. All analyses were performed in CLC Genomics Workbench version 11.0.

To our knowledge, this is the first reported full polyprotein coding sequence of O/ME-SA/Ind2001e from southern Vietnam. The 7,787-nt partial genome encodes a 6,999-nt open reading frame (ORF) flanked by a 696-nt 5′ untranslated region (UTR) and a 91-nt 3′ UTR. The single ORF encodes a polyprotein posttranslationally processed into structural proteins VP1 through VP4 and nonstructural proteins Lpro, 2A, 2B, 2C, 3A, 3B, 3C, and 3D. Similar to the data provided in the World Reference Laboratory for FMD (WRLFMD) VP1 sequence reports (5–7), O/VIT/8338/2017 has highest similarity (98.32%) to BAN/Gka-236(pig)2015 (GenBank accession number KX712091) obtained from a vesicular lesion of a pig from Bangladesh in April 2015 (9). The 131-nt differences between the aforementioned sequences translate to 23 amino acid differences divided between Lpro (n = 3), 1B (n = 2), 1C (n = 3), 1D (n = 1), 2 C (n = 1), 3A (n = 7), 3B (n = 2), 3C (n = 1), and 3D (n = 3). No nucleotide insertions or deletions are present between the two genomes.

The Ind2001e sublineage has been detected in Bhutan (4), China (2), Malaysia (10), Sri Lanka (2), Vietnam (2), and Jordan (1, 5–7). Although numerous FMDV viruses circulate in Vietnam, including O/ME-SA/Ind2001d, the emergence of this novel sublineage may impact FMDV control strategies (10). The rapid evolution and widespread distribution of FMDV in Vietnam highlight the importance of epidemiological detection of FMDV/O/VIT/8338/2017 in Vietnam.

Data availability.

The complete genome nucleotide sequence has been deposited in GenBank as O/VIT/8338/2017 under accession number MH891503. This report describes version MH891503.1.