TABLE 1.
Genomic regions and PCR primers used for targeted resequencing of SNVs
| Genomic region | Primer name | Primer sequence | Genome region amplified | SNV nucleotide position: amino acid changea |
|---|---|---|---|---|
| Block C | C-f | CAACTTCGCGGGTATGAATC | LORF2 (MDV012) | 17359: promoter |
| C-r | ACGCTCCCTAGATCGACTCC | 17521: synonymous | ||
| 17545: intronic | ||||
| Block D | D-f | ACGGCCATTTTTAGTTCGTG | UL5 (MDV017) | 23201: I682R |
| D-r | TGCGAAATTAGAAGCCAAC | |||
| Block Pre-E | Pre-E-f | CCGTATGACAGCGAACAAAG | UL41 (MDV054) | 98690: R17stop |
| Pre-E-r | CATCTGGCTAAGCTATGTGCAA | |||
| Block E | E-f | CATTAAACAAACAACAATTGAGC | UL42 (MDV055) and UL43 (MDV056) | 100014: D207G |
| E-r | GCCAAGATGTGAACAACGATT | 101786: A375T | ||
| Block F | F-f | AGAGAAACCAACGCGACAAT | UL46 (MDV059) | 106639: Q117R |
| F-r | ATAATGAAGCGGCTCAGCTC | |||
| Block B/G | G-f | AAATTCGCACTTGAGTGTTGG | Between R-LORF11 and R-LORF12 | 12990/128612: intergenic |
| G-r | TCTCATGAAACATACCCCTTCC | 12986/128616: intergenic | ||
| 12114/129489: intergenic | ||||
| Block I | I-f | TCAATCACATATATGGGTCTCAGG | ICP4 (MDV084/MDV100) | 145864/178590: S1630P |
| I-r | TCGCGTGGTATCACTGATTG | |||
| Block J | J2-f | CAGGTGAGGTGGAAGTAGG | ICP4 (MDV084/MDV100) | 149985/174469: L256S |
| J2-r | CTGTTCATGTCGGAGGTCTG | 150169/174285: T195A | ||
| 150563/173891: Q63H | ||||
| 150567/173887: G62V |
a
Nucleotide position in Md5B40BAC-c1 reference genome HQ149525.1 followed by amino acid change and its position in protein. SNVs in repeat genes have both equivalent positions listed within internal repeat long (IRL)/terminal repeat long (TRL) or internal repeat short (IRS)/terminal repeat short (TRS) indicated.