There is also a 3 nt deletion (nt 25201–25203) in the residual ORF3 coding sequence within the FLI strain which would make for an in-frame deletion but since the initiation codon is lost then this is probably not significant.
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Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs.
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