ABSTRACT
Here, we report near-complete genome sequences of three foot-and-mouth disease viruses isolated in 2016 from bovine and porcine epithelial tissue samples collected in Nonthaburi, Songkhla, and Ratchaburi provinces, Thailand. These viruses were classified as serotype O, topotype ME-SA, and sublineage Ind-2001e.
ANNOUNCEMENT
Foot-and-mouth disease (FMD) virus (FMDV; Aphthovirus, Picornaviridae) causes FMD, which is the most contagious disease of cloven-hoofed mammals, characterized by vesicles on the feet and in oral cavities (1). FMD is endemic in Asia, the Middle East, and Africa (2). The single-stranded FMDV genome is a positive-sense 8,400-base RNA. Seven serotypes (O, A, C, Asia 1, and SAT 1 to 3) have genetically divergent topotypes, lineages, and sublineages (3). Although serotype O in Southeast Asia comprises the Cathay, Southeast Asia, and Middle East-South Asia (ME-SA) topotypes (2), the Ind-2001e sublineage within the ME-SA topotype is currently the most predominant (4).
FMDVs O/TAI/269-2/2016, O/TAI/315/2016, and O/TAI/317-3/2016 were isolated in 2016 from animals with typical FMD symptoms in Thailand by using primary lamb kidney cells and then passaged three times in ZZ-R 127 and IB-RS-2 cells (5, 6) (Table 1). Once samples were collected, viruses were isolated immediately and stored at −80°C until RNA extraction. RNAs were extracted from cell culture supernatants using a High Pure viral RNA kit (Roche Diagnostics). Near-complete viral genomes (approximately 7.7 kb) were amplified using a SuperScript IV one-step reverse transcription-PCR (RT-PCR) system (Life Technologies) and two FMDV-specific primer sets (7). Libraries were prepared using an Ion Xpress Plus fragment library kit (Life Technologies). DNAs were fragmented for 8 min to generate average 300-bp fragments, which were barcoded using Ion Xpress barcodes (Life Technologies). Libraries were sequenced using an Ion Torrent PGM sequencer (Life Technologies), 314v2 chip, and Ion PGM sequencing 200 kit version 2 (Life Technologies). Torrent suite software version 5.0.5 (Life Technologies) yielded total reads as follows: 67,779 (15,198,038 bp), O/TAI/269-2/2016; 44,701 (9,639,561 bp), O/TAI/315/2016; and 32,699 (6,594,969 bp), O/TAI/317-3/2016. These were assembled and mapped using the PathogenAnalyzer software version 1.2 with default parameters (minimum coverage, 15; minimum coverage for mixed calls, 40; minimum coverage for indels, 40; minimum fraction for mixed calls, 0.2; minimum fraction for out-of-frame indels, 0.75) (Life Technologies). Final assemblies of O/TAI/269-2/2016, O/TAI/315/2016, and O/TAI/317-3/2016 comprised 7,692, 7,692, and 7,694 nucleotides (nt); 53.45%, 53.52%, and 53.46% G+C contents; and 1,976, 1,253, and 857.4 average coverage depths, respectively.
TABLE 1.
Information about isolates
| Isolate | Province | District | Subdistrict | Species | Lesion site | Collection date (day/mo/yr) |
|---|---|---|---|---|---|---|
| O/TAI/269-2/2016 | Nonthaburi | Bang Khu Rat | Bang Bua Thong | Cattle | Lip | 13/10/2016 |
| O/TAI/315/2016 | Songkhla | Sadao | Padang Besor | Cattle | Tongue | 8/11/2016 |
| O/TAI/317-3/2016 | Ratchaburi | Ban Pong | Nong Or | Pig | Nose | 10/11/2016 |
Genome sequences of O/TAI/269-2/2016, O/TAI/315/2016, and O/TAI/317-3/2016 were the most closely related to those of O/VIT/20/2016 (GenBank accession number MG983741) (8), O/MYA/Yan/3/2016 (GenBank accession number LC438822) (9), and O/VIT/20/2016 (8) with 99.64%, 99.25%, and 99.47% nucleotide sequence identity rates, respectively, according to NCBI BLASTn analysis (analyzed on 18 October 2022 at http://blast.ncbi.nlm.nih.gov/Blast.cgi). These genomes were classified as O/ME-SA/Ind-2001e by phylogenetic analysis together with sequences obtained from the GenBank database (Fig. 1).
FIG 1.
Phylogenetic analysis of VP1 sequences of three FMDV isolates in this study. VP1 sequences of FMDV isolates were used for phylogenetic analysis using a maximum likelihood method with default parameters in MEGA version 10.2.0 (https://www.megasoftware.net/). Horizontal distances are proportional to the minimum number of nucleotide differences required to join nodes and sequences. The isolates in this study are marked by red squares. The reference strains of each topotype/lineage are shown along with GenBank accession numbers after each strain name.
The near-complete genome sequences of three O/ME-SA/Ind-2001e FMDVs determined here will contribute to efforts to monitor epidemiological information concerning outbreaks and to implement appropriate countermeasures.
Data availability.
The nucleotide sequences of the three FMDVs reported here were deposited in GenBank under accession numbers LC729870, LC729871, and LC729872. Raw sequence reads were deposited in the DDBJ Sequence Read Archive (DRA) under BioProject accession number PRJDB14377 and DRA Run accession number DRR408791 (O/TAI/269-2/2016), BioProject accession number PRJDB14378 and DRA Run accession number DRR408792 (O/TAI/315/2016), and BioProject accession number PRJDB14379 and DRA Run accession number DRR408793 (O/TAI/317-3/2016).
ACKNOWLEDGMENTS
This study was conducted as a component of the research project on “Regulatory research projects for food safety, animal health and plant protection (JPJ008617, 18065101)” funded by the Ministry of Agriculture, Forestry and Fisheries of Japan. The Agriculture Research Development Agency (Public Organization, Thailand) also funded this study.
Contributor Information
Kazuki Morioka, Email: morioka@affrc.go.jp.
Simon Roux, DOE Joint Genome Institute.
REFERENCES
- 1.Diaz-San Segundo F, Medina GN, Stenfeldt C, Arzt J, de Los Santos T. 2017. Foot-and-mouth disease vaccines. Vet Microbiol 206:102–112. doi: 10.1016/j.vetmic.2016.12.018. [DOI] [PubMed] [Google Scholar]
- 2.King D, Di Nardo A, Henstock M. 2020. OIE/FAO foot-and-mouth disease reference laboratory network annual report 2020. https://www.wrlfmd.org/sites/world/files/quick_media/OIE-FAO%20FMD%20Ref%20Lab%20Network%20Report%202020.pdf.
- 3.Knowles NJ, Samuel AR. 2003. Molecular epidemiology of foot-and-mouth disease virus. Virus Res 91:65–80. doi: 10.1016/S0168-1702(02)00260-5. [DOI] [PubMed] [Google Scholar]
- 4.Purevsuren B. 2022. Regional FMD situation. 25th SEACFMD National Coordinators Meeting. World Organization for Animal Health, Bali, Indonesia. https://rr-asia.woah.org/wp-content/uploads/2022/10/4-regional_fmd-situation_bp.pdf.
- 5.Brehm KE, Ferris NP, Lenk M, Riebe R, Haas B. 2009. Highly sensitive fetal goat tongue cell line for detection and isolation of foot-and-mouth disease virus. J Clin Microbiol 47:3156–3160. doi: 10.1128/JCM.00510-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Chapman WG, Ramshaw IA. 1971. Growth of the IB-RS-2 pig kidney cell line in suspension culture and its susceptibility to foot-and-mouth disease virus. Appl Microbiol 22:1–5. doi: 10.1128/am.22.1.1-5.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Nishi T, Yamada M, Fukai K, Shimada N, Morioka K, Yoshida K, Sakamoto K, Kanno T, Yamakawa M. 2017. Genome variability of foot-and-mouth disease virus during the short period of the 2010 epidemic in Japan. Vet Microbiol 199:62–67. doi: 10.1016/j.vetmic.2016.12.025. [DOI] [PubMed] [Google Scholar]
- 8.Bachanek-Bankowska K, Di Nardo A, Wadsworth J, Mioulet V, Pezzoni G, Grazioli S, Brocchi E, Kafle SC, Hettiarachchi R, Kumarawadu PL, Eldaghayes IM, Dayhum AS, Meenowa D, Sghaier S, Madani H, Abouchoaib N, Hoang BH, Vu PP, Dukpa K, Gurung RB, Tenzin S, Wernery U, Panthumart A, Seeyo KB, Linchongsubongkoch W, Relmy A, Bakkali-Kassimi L, Scherbakov A, King DP, Knowles NJ. 2018. Reconstructing the evolutionary history of pandemic foot-and-mouth disease viruses: the impact of recombination within the emerging O/ME-SA/Ind-2001 lineage. Sci Rep 8:14693. doi: 10.1038/s41598-018-32693-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Maung WY, Nishi T, Kato T, Lwin KO, Fukai K. 2019. Genome sequences of foot-and-mouth disease viruses of serotype O linages Mya-98 and Ind-2001d isolated from cattle and buffalo in Myanmar. Microbiol Resour Announc 8:e01737-18. doi: 10.1128/MRA.01737-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The nucleotide sequences of the three FMDVs reported here were deposited in GenBank under accession numbers LC729870, LC729871, and LC729872. Raw sequence reads were deposited in the DDBJ Sequence Read Archive (DRA) under BioProject accession number PRJDB14377 and DRA Run accession number DRR408791 (O/TAI/269-2/2016), BioProject accession number PRJDB14378 and DRA Run accession number DRR408792 (O/TAI/315/2016), and BioProject accession number PRJDB14379 and DRA Run accession number DRR408793 (O/TAI/317-3/2016).