Evaluating the potential of whole-genome sequencing for tracing transmission routes in experimental infections and natural outbreaks of bovine respiratory syncytial virus

Table 3 Characteristics of variation among consensus sequences among experimental samples

Experiment	Genome position	Gene	Gene position	A.a. position	Codon/base change	A.a. change	Freq. in challenge
C	9328	L CDS	922	305	GAC → GTC	Asp → Val	39.6%
D	3413	M CDS	203	65	CTA → CCA	Leu → Pro	14.9%
F	589	NS2 5′-UTR	9	–	C → A	–	14.9%
F	4855	G CDS	166	51	ATG → TTG	Met → Leu	17.5%
F	5819	F CDS	263	84	AAA → GAA	Lys → Glu	40.0%
F	6630	F CDS	1074	354	CTG → CAG	Leu → Gln	20.9%
F	7651	M2 CDS	138	43	CTG → CTA	Synonymous	23.3%
F	9328	L CDS	922	305	GTC → GAC	Val → Asp	16.0%
F	12089	L CDS	3683	1226	AAT → GAT	Asn → Asp	31.1%

Nucleotide position and amino acid (a.a.) position are relative to NCBI Reference Sequence NC_038272.1 (BRSV ATCC51908 complete genome). Codon, base and a.a. changes are relative to the experimental challenge virus consensus sequence.
CDS: coding sequence, UTR: untranslated region.

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