TABLE 4.
Recombination breakpoint analysis of full ILTV genome sequences and field isolates from Asia, Australia, and the United States and in vivo recombinants
| Origin of isolates | Breakpoint (in alignment), 99% CIa |
Gene(s) at the beginning of the breakpoint locationb | Gene(s) at the end of the breakpoint locationb | Possible viruses involved in recombination eventc | Method(s) by which breakpoint was detected in RDP4 | |
|---|---|---|---|---|---|---|
| Beginning | End | |||||
| Asia (China) | 106423–109054 | 125644–129391 | UL4, UL3.5, UL3, UL2, UL1 | US10, sORF4 | R, WG; M, unknown; m, K317 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ |
| 43560–45099 | 45674–54215 | UL28, UL29 | UL29, UL30, UL31, UL32, UL33, UL34 | R, K317; M, SERVA; m, WG | RDP, GENECONV, Bootscan, MaxChi, Chimaera, 3SEQ | |
| Australia | 27228–28747 | 112173–113630 | ORFB, ORFC | UL[−1] | R, CL9; M, SERVA; m, A20 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ |
| 114752–115584 | 139504–140702 | No gene between UL[−1] and ICP4 | US6, US7 | R, CL10; M, ACC78; m, SA2 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ | |
| 30261–31965 | 51062–60138 | ORFE, UL22 | UL30, UL31, UL32, UL33, UL34, UL35, UL36 | R, CL10; M, SERVA; m, A20 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ | |
| 134126–137622 | Undetermined | US6, US7 | Undetermined | R, CL9; M, unknown; m, V1-99 | RDP, GENECONV, MaxChi, Chimaera, SiScan, 3SEQ | |
| 113596–114071 | 120150–124890 | No gene between UL[−1] and ICP4 | US10 | R, CL9; M, unknown; m, CSW-1 | RDP, MaxChi, Chimaera, SiScan, 3SEQ | |
| 111500–113586 | 113598–126007 | No gene between UL[−1] and ICP4 | ICP4, US10 | R, C10; M, CSW-1; m, SA2 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, 3SEQ | |
| 30804–33011 | 43052–49251 | ORFE, UL22 | UL28, UL29, UL30 | R, ACC78; M, SERVA; m, SA2 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ | |
| 99353–101053 | 104765–107587 | UL8 | UL5, UL4, UL3.5 | R, CL10; M, SERVA; m, A20 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ | |
| 112731–113586 | 114079–114296 | UL[−1] | No gene between UL[−1] and ICP4 | R, V1-99; M, unknown; m, SA2 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ | |
| 126079–126160 | 126204–126250 | No gene | No gene | R, A20; M, SA2; m, SERVA | GENECONV, 3SEQ | |
| Europe (Italy) | 42226–117783 | 122731–126724 | Entire UL region | Entire US region | R, Nobilis; M, SERVA; m, 757/11 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, 3SEQ |
| United States | 113909–114632 | 122256–124629 | No gene between UL[−1] and ICP4 | No gene | R, 1874c5; M, J2; m, unknown | RDP, GENECONV, Bootscan, MaxChi, Chimaera, 3SEQ |
| 111754–112964 | 113276–127469 | UL[−1] | ICP4, US10 | R, USDA; M, 81658; m, unknown | RDP, GENECONV, Bootscan, MaxChi, Chimaera, 3SEQ | |
| 115821–119810 | 120055–121242 | ICP4 | No gene | R, BdORFC; M, 6.48.88; m, unknown | RDP, GENECONV, Bootscan, MaxChi, Chimaera, 3SEQ | |
| 117501–119320 | 120028–121127 | ICP4 | No gene | R, 81658; M, unknown; m, 6.48.88 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, 3SEQ | |
| 45501–49291 | 50588–59726 | UL29, UL30 | UL30, UL31, UL32, UL33, UL34, UL35, UL36 | R, S2.86; M, unknown; m, USDA | RDP, GENECONV, 3SEQ | |
| 81577–89884 | 90133–95942 | UL19, UL13, UL15, UL17, UL14 | UL13, UL12, UL11, UL10 | R, 6.48.88; M, S2.816; m, J2 | RDP, GENECONV, Bootscan, 3SEQ | |
| 107225–122304 | 122306–128723 | UL 3.5, UL2, UL1, UL0, UL[−1], ICP4 | US10, Sorf4, US2, US3 | R, J2; M, unknown; m, 3.26.90 | GENECONV | |
| 22886–24681 | 24683–26851 | UL46, UL45 | UL45, ORFA, ORFB | R, 6.48.88; M, unknown; m, 14.939 | GENECONV, MaxChi | |
| 14052–16151 | 16153–18973 | UL52 | UL52, UL51, UL50 | R, 6.48.88; M, unknown; m, BdORFC | GENECONV | |
| 1–26560 | 1–26560 | UL56, ORFF, UL54, UL53, UL52, UL50, UL49.5, UL49, UL48, UL46, UL45 | UL56, ORFF, UL54, UL53, UL52, UL50, UL49.5, UL49, UL48, UL46, UL45 | R, USDA; M, 14.939; m, Laryngovac | RDP, MaxChi, SiScan | |
| 42685–50586 | 50591–66866 | UL28, UL29, UL30, UL31 | UL32, UL33, UL34, UL35, UL36, UL37 | R, 1874c5; M, J2; m, unknown | GENECONV, Bootscan | |
| In vivo recombinants | 53623–68876 | 120517–121888 | UL35, UL36, UL37, UL38, UL39 | No gene between UL [−1] and ICP4 | R, sample 23; M, unknown; m, CSW-1 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ |
| 121902–124017 | 134435–137336 | US10, SORF3 | US6, US7, US8 | R, sample 27; M, V1-99; m, unknown | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ | |
| 71911–78480 | 112397–120377 | UL42, UL43, UL44, UL21, UL20 | ICP4 | R, sample 15; M, V1-99; m, CSW-1 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, SiScan, 3SEQ | |
| 121904–125713 | 129197–137424 | US10, protein SORF3, US2, US3 | US4, US5, US6, US7, US8 | R, sample 15; M, V1-99; m, sample 23 | GENECONV, Bootscan, 3SEQ | |
| 74976–97499 | 111841–114434 | UL44, UL21, UL20, UL19, UL18, UL15, UL17, UL14, UL13, UL12, UL11, UL10, UL9 | No gene Between UL [-1] and ICP4 | R, sample 12; M, sample 1; m, V1-99 | RDP, GENECONV, Bootscan, MaxChi, Chimaera, 3SEQ | |
| 2256–97499 | 106970–137424 | Entire UL region | Entire US region | R, sample 12; M, unknown; m, V1-99 | GENECONV, MaxChi, Chimaera | |
| 1–32193 | 105020–137424 | UL56, protein IF, UL54, UL53, UL52, UL51, UL50, UL49.5, UL49, UL48, UL46, UL45, protein IA-IB-IC-ID-IE, UL22 | Entire US region | R, sample 12; M, unknown; m, V1-99 | GENECONV, MaxChi, Chimaera, 3SEQ | |
| 1–1909 | 5870–17769 | No gene | UL56, protein IF, UL54, UL53, UL52, UL51, UL50 | R, sample 23; M, sample 1; m, sample 12 | SiScan | |
| 1–53621 | 107559–120122 | UL56, protein IF, UL54, UL53, UL52, UL51, UL50, UL49.5, UL49, UL48, UL46, UL45, protein IA-IB-IC-ID-IE, UL22, UL24, UL25, UL26, UL26.5, UL27, UL28, UL29, UL30, UL31, UL32, UL33, UL34 | Entire US region | R, V1-99; M, unknown; m, sample 8 | GENECONV, MaxChi, SiScan, 3SEQ | |
| 1–137424 | 1–137424 | Entire UL region | Entire UL region | R, sample 12; M, CSW-1; m, sample 27 | GENECONV, Bootscan, MaxChi, 3SEQ | |
| 1–113123 | 1–113123 | Entire UL region | Entire UL region | R, sample 27; M, V1-99; m, sample 23 | RDP, GENECONV, MaxChi, Chimaera | |
| 1–17769 | 19248–137424 | UL56, protein IF, UL54, UL53, UL52, UL51, UL50 | UL48, UL46, UL45, protein IA-IB-IC-ID-IE, UL22, UL24, UL25, UL26, UL26.5, UL27, UL28, UL29, UL30, UL31, UL32, UL33, UL34 | R, CSW-1; M, sample 15; m, sample 27 | MaxChi, Chimaera, 3SEQ | |
| 1–137424 | 1–137424 | Entire UL and US regions | Entire UL and US regions | R, sample 8; M, sample 15; m, unknown | GENECONV, MaxChi, 3SEQ | |
| 11775–17921 | 17923–137424 | UL53, UL52, UL51, UL50, UL49.5 | UL49, UL48, UL46, UL45, protein IA-IB-IC-ID-IE, UL22, UL24, UL25, UL26, UL26.5, UL27, UL28, UL29, UL30, UL31, UL32, UL33, UL34 | R, sample 27; M, sample 8; m, unknown | MaxChi, 3SEQ | |
| 1–137424 | 1–137424 | Entire UL and US regions | Entire UL and US regions | R, sample 15; M, sample 1; m, unknown | 3SEQ | |
a
CI, confidence interval.
b
UL, unique long; US, unique short.
c
R, recombinant; M, major parent; m, minor parent.