Genome Sequences of 18 Foot-and-Mouth Disease Virus Outbreak Strains of Serotype O Sublineage Ind2001d from India, 2013 to 2014

Abstract

We report the full polyprotein-coding sequences and partial untranslated regions (UTRs) of 18 foot-and-mouth disease (FMD) viruses from 4 outbreaks in India in 2013 and 2014. All strains grouped within the O/ME-SA/Ind2001d sublineage. These genomes update knowledge of FMD virus (FMDV) diversity in South Asia and may contribute to molecular epidemiology studies and vaccine selections.

Use of Slaughterhouses as Sentinel Points for Genomic Surveillance of Foot-and-Mouth Disease Virus in Southern Vietnam

“…Samples from 2013-2015 were sequenced using the Sanger method, as previously described [5], to obtain VP1 sequences, or, by next-generation sequencing (NGS), to obtain full open reading frame (ORF) sequences. For NGS-derived sequences, overlapping RT-PCR amplicons covering the full ORF were produced using three sets of primers [23], and amplicons were sequenced as previously described [26]. Samples from 2016-2017 were sequenced by NGS of RT-PCR amplicons covering the P1 region, as previously described [27].…”

Novel Recombinant Foot-and-Mouth Disease Virus Circulating in Vietnam

“…FMDV was confirmed by virus isolation (VI) on LFBKαvβ6 cells, followed by detection of viral RNA in VI supernatant by real-time reverse transcription PCR (qRT-PCR) ( 6 , 7 ). VI supernatant RNA was subjected to viral deep sequencing as previously described ( 8 , 9 ). Briefly, RNA was extracted using the MagMAX total RNA isolation kit, and host DNA was depleted using the DNA-free DNase kit (Ambion).…”

Genome Sequences of Four Foot-and-Mouth Disease Virus SAT 1 Topotype X Isolates from Cameroon

“…FMDV was confirmed by detection of viral RNA in tissue homogenate using FMDV-specific real-time reverse transcriptase PCR (rRT-PCR) and by virus isolation (VI) on LFBK-α v β 6 cells followed by rRT-PCR of VI supernatant (7, 8). Tissue homogenate or VI supernatant RNA was extracted (MagMAX total RNA isolation kit; Thermo Fisher) and DNase treated (DNA-free DNase kit; Ambion) and then subjected to viral deep sequencing as described (9, 10). Briefly, RNA underwent first-strand synthesis using the Superscript II first-strand synthesis system (Invitrogen) with random primers and two FMDV-specific primers.…”