TABLE 1.

Primers^a

Primer	Sequence	Location
ISHp609 primers
609LE	CATTAAACTTTCAATTTAATTTTG	At the left end, forward
609R-t1	CTAAAAACTCTTTAATCTTATTAAAAGTA	At the right end, reverse
609.F1	CACAACAGGTATTAATGCTT	1,083 bp from the right end, in orfB, forward
609.R1	CTTTAGCTCTTGTTTCCAGC	1,985 bp from the left end, in orfB, reverse
609t2-1b	TTACCTGCAAGCCATTAAGG	1,037 bp from the right end, in orfB, forward
609t2-2b	TTATGCATAAAGTTATTCAGC	1,535 bp from the left end, in orfB, reverse
FlankL	CTTTATTTGGGAGATTTAGAAGC	2,266 bp from the right end, in orf1, forward
609.R6	CCATTCTGCAATAATAGCTTCTC	346 bp from the left end, in orf2, reverse
609R3t1	TAAATAGCTTTTCTACTAACTCATA	1,001 bp from the left end, in orfA, reverse
609.R5	ATTAGCGTAGTTGTAAAGGTT	1,199 bp from the left end, in orfB, reverse
Other primers
jhp959	GTAGCACAACTCTTATGCGATG	177 bp from the 3′ end of jhp959, forward
jhp962	TGTATGTCATGCTGAGCGAAAAC	371 bp from the 3′ end of jhp962, reverse
CR2-LF	CATACTAGACTTAAAGGACAGCA	Left of ISHp609 in CR2 clonec
CR2-RF	ATTTTGATTTTGTCTGTTACTTCGCAC	Right of ISHp609 in CR2 clonec
B43-LF	GCTATGGCAGAAAACATCTAT	Left of ISHp609 in HUP-B43
B43-RF	GAGTTTCTAAATAATTCTCAT	Right of ISHp609 in HUP-B43
B79-LF	CAGATTTACCCAAACTCACT	Left of ISHp609 in HUP-B79
B79-RF	AAGGTTTTATCAAAGCCTATGC	Right of ISHp609 in HUP-B79
LitA7-LF	GAGGTAATTTTTGAAATTTTAACAC	Left of ISHp609 in LitA7
LitA7-RF	ATCAGGCTTTAGGGTATTCTTT	Right of ISHp609 in LitA7
LitA38-LF	TTTATCCTTTCTTTATTATTAAACTTTC	Left of ISHp609 in LitA38
LitA38-RF	ATTTTATGCGATTGCATTGAAAG	Right of ISHp609 in LitA38

^aSequences of additional primers used for sequencing are available on request.

^bISHp609var specific (Chennai4 strain).

^cSee reference 6.