Table 1 Putative recombinant strains (n = 25) detected by the RDP4 method with a default setting (window size = 30).
Accession # | Strain | Recombination region (nucleotide) | Corresponding ORF region | Parental strain | % similarity |
|---|---|---|---|---|---|
KC164505 | England-1_2012 | 22965–24618 | S | KM027262_Riyadh-683-KSA_2014 | 99.5 |
KC667074 | Enland-Qatar_2012 | 22602–24618 | S | KF600620_Bisha-1_2012 | 99.5 |
KF600613 | Riyadh-3_2013 | 22965–25594 | S | KM027262_Riyadh-683-KSA_2014 | 99.4 |
KF600628 | Hafr-Al-Batin-1_2013 | 231–1532 | ORF1a | NC019843_HCoV-EMC_2012 | 99.8 |
KF958702 | Jeddah-1_2013 | 22965–26708 | S, ORF3, ORF4a, ORF4b, ORF5 | KM027262_Riyadh-683-KSA_2014 | 99.5 |
KF961221 | Qatar-3_2013 | 1–1532; 28497–29529 | ORF1a, N, ORF8b | NC019843_HCoV-EMC_2012 | 99.8 |
KF961222 | Qatar-4_2013 | 231–1532 | ORF1a | NC019843_HCoV-EMC_2012 | 99.9 |
KJ156881 | Wadi-Ad-Dawasir-1_2013 | 22965–25594 | S | KM027262_Riyadh-683-KSA_2014 | 99.4 |
KJ156934 | Riyadh-14_2013 | 231–1532 | ORF1a | NC019843_HCoV-EMC_2012 | 99.9 |
KJ156944 | Riyadh-5_2013 | 22965–26708 | S, ORF3, ORF4a, ORF4b, ORF5 | KM027262_Riyadh-683-KSA_2014 | 99.5 |
KJ156949 | Taif-1_2013 | 22965–25594 | S | KM027262_Riyadh-683-KSA_2014 | 99.5 |
KJ556336 | Jeddah-1_2013 | 22963–26706 | S, ORF3, ORF4a, ORF4b, ORF5 | KM027262_Riyadh-683-KSA_2014 | 99.5 |
KJ829365 | Florida-USA-2-Saudi Arabia_2014 | 22964–24397 | S | KM027262_Riyadh-683-KSA_2014 | 99.3 |
KM027255 | Jeddah-C7149-KSA_2014 | 22965–24397 | S | KM027262_Riyadh-683-KSA_2014 | 99.4 |
KM027256 | Jeddah-C7569-KSA_2014 | 22965–24397 | S | KM027262_Riyadh-683-KSA_2014 | 99.4 |
KM027257 | Jeddah-C7770-KSA_2014 | 22965–28690 | S, ORF3, ORF4a, ORF4b, ORF5, E, M, N, ORF8b | KM027262_Riyadh-683-KSA_2014 | 99.7 |
KM027258 | Jeddah-C8826-KSA_2014 | 22759–24397 | S | KM027262_Riyadh-683-KSA_2014 | 99.4 |
KM027259 | Jeddah-C9055-KSA_2014 | 22965–24397 | S | KM027262_Riyadh-683-KSA_2014 | 99.4 |
KM027260 | Jeddah-C10306-KSA_2014 | 22965–24397 | S | KM027262_Riyadh-683-KSA_2014 | 99.4 |
KM027261 | Makkah-C9355-KSA_2014 | 22965–24397 | S | KM027262_Riyadh-683-KSA_2014 | 99.4 |
KP223131 | Florida-USA-2-Saudi Arabia_2014 | 22964–24397 | S | KM027262_Riyadh-683-KSA_2014 | 99.3 |
KT006149 | China-GD01_2015 | 1–1532; 28054–29529 | ORF1a, M, N, ORF8b | NC019843_HCoV-EMC_2012 | 99.8 |
18033–23502 | ORF1b, S | KF958702_Jeddah-1_2013 | 99.9 | ||
KT026455 | Riyadh-KSA-2959_2015 | 1–1532; 28497–29529 | ORF1a, N, ORF8b | NC019843_HCoV-EMC_2012 | 99.8 |
17424–23502 | ORF1b, S | KF958702_Jeddah-1_2013 | 99.9 | ||
KT026456 | Riyadh-KSA-4050_2015 | 1–1532; 28497–29529 | ORF1a, N, ORF8b | NC019843_HCoV-EMC_2012 | 99.7 |
18033–23502 | ORF1b, S | KF958702_Jeddah-1_2013 | 99.9 | ||
KT029139 | KOR-KNIH-002_2015 | 1–1532; 28055–29520 | ORF1a, M, N, ORF8b | NC019843_HCoV-EMC_2012 | 99.8 |
18033–23502 | ORF1b, S | KF958702_Jeddah-1_2013 | 99.9 |
