TABLE 4.

Unique significant variants (>1%) common for set a and b for primary infection cases taking as a reference the first isolate obtained during the Cuban epidemic, 2001 to 2002

Sample no.	Feature	Position (nt)c	Reference allele	Set a variant				Set b variant
				Allele	Amino acid no.	Change	Frequency (%)	Allele	Amino acid no.	Change	Frequency (%)
9	−a	−	−	−	−	−	−	−	−	−	−
10	NS1	3424	C	T	344	Synonymous → N	1.145	T	344	Synonymous → N	1.037
	NS1	2887	C	T	165	Synonymous → T	1.079	T	165	Synonymous → T	0.966
12	NS5	9803	C	T	754	Synonymous → L	4.539	T	754	Synonymous → L	4.371
	NS5	7866	C	T	108	P → L	1.538	T	108	P → L	1.536
14	NS1	2924	C	T	178	Synonymous → L	5.312	T	178	Synonymous → L	6.398
	NS3	5371	C	T	293	Synonymous → A	1.086	T	293	Synonymous → A	0.134
18	3′ UTR	10369	G	T	*b	*	1.641	T	*	*	2.097
22	−	−	−	−	−	−	−	−	−	−	−

^aMinority variants represent <1%.

^bIndicates position in noncoding region of the 3′ untranslated region (UTR).

^cnt, nucleotide.