Fig. 1
Sampling area
Table 1
Oligonucleotide data used in the study
| Virus | Name | Sequence | Amplicon size (bp) | Location | Reference |
|---|---|---|---|---|---|
| Nebo2F | TYTAYGACGGGCGCTWTTATGG | ||||
| Nebovirus | Nebo1R | AGACAGTGCCGAAAAGGGTGTA | 282 | 4984–5265a | This study |
| BoNoV851-F | ATGTGGTVCAGGCNAACAGCTA | ||||
| BoNoV1350-R | ACTACCTTCCCACARHGACARA | 500 | 4538–5037b | This study | |
| Norovirus | IIIBovNo-F | CGCTCCATGTTYGCBTGG | |||
| IIIBovNo-R | ATCAGCACATGRGGRAACTG | 516 | 4972–5487c | (13) |
[i] a Genbank accession number AY082891; bGenbank accession number AY126474; c Genbank accession number AJ011099
Table 2
GenBank accession numbers of noro- and nebovirus strains used in genetic analysis
| Genus | Strain | Accession number | Genotype |
|---|---|---|---|
| Mu/NoV/GV/MNV1/2002/USA | AY228235.2 | GV | |
| NLV/SaintCloud/624/1998/US | AF414427.1 | GIV. 1 | |
| NLV/Brattleboro/321/1995/US | AF414415.1 | GII.3 | |
| Toronto/ CAN | U02030 | GII.3 | |
| SOV/ UK | L07418 | GI.2 | |
| NV/USA | M87661 | GI.1 | |
| Bo/Thirsk10/00/UK | AY126468.2 | GIII. 1 | |
| Bo/Jena/DE | AJ011099 | GIII. 1 | |
| Bo/ DuzceN2/2010/TUR | KF218823.1 | GIII.2 | |
| Bo/SivasN6/2011/TUR | KF218824.1 | GIII.2 | |
| bovine/ DijonA077/06/FR | GU259577.1 | GIII.2 | |
| bovine/ DijonA436/08/FR | GU259579.1 | GIII.2 | |
| Bo/Newbury2/1976/UK | AF097917.5 | GIII.2 | |
| Bo/NoV/JN-MA156/04/Korea | DQ912792.1 | GIII.2 | |
| Bo/ Dumfries/94/UK | AY126474.2 | GIII.2 | |
| Bo/AdiyamanN6/2011/TUR | KF218825.1 | GIII.2 | |
| Bo/BalikesirN9/2009/TUR | KF218822.1 | GIII.2 | |
| bovine/GIII.2/471_0790/2005/NOR | FM242193.1 | GIII.2 | |
| bovine/GIII.2/718_0785/2006/NOR | FM242191.1 | GIII.2 | |
| bovine/GIII.2/312_0529/2006/NOR | FM242186.1 | GIII.2 | |
| bovine/GIII.2/240_0243/2005/NOR | FM242189.1 | GIII.2 | |
| Bo/Nov-33/USA/2010 | JN585051.1 | GIII.2 | |
| BoNoV/ Bolat7/2016/TR | MG022084 | GIII.2 | |
| BoNoV/Bolat85/2016/TR | MG022085 | GIII.2 | |
| Bo/Nov-45/USA/2010 | JN585060.1 | GIII.2 | |
| Bo/Nov-6/USA/2010 | JN585033.1 | GIII.2 | |
| Norovirus | Bo/Nov-16/USA/2010 | JN585041.1 | GIII.2 |
| Bo/Nov-10/USA/2010 | JN585036.1 | GIII.2 | |
| Bo/Nov-2/USA/2010 | JN585029.1 | GIII.2 | |
| Bo/Nov-1/USA/2010 | JN585028.1 | GIII.2 | |
| Bo/Nov-13/USA/2010 | JN585038.1 | GIII.2 | |
| Bo/NoV/JN-MA140/04/Korea | DQ912791.1 | GIII.2 | |
| Bo/NoV/JN-MA302/04/Korea | DQ912797.1 | GIII.2 | |
| Bo/NoV/JN-MA271/04/Korea | DQ912795.1 | GIII.2 | |
| Bo/NoV/JN-SA296/04/Korea | DQ912796.1 | GIII.2 | |
| bovine/ DijonA407/08/FR | GU259575.1 | GIII.2 | |
| Bo/MonastirB139/2009/TUN | JN418489.1 | GIII.2 | |
| bovine/Belgium/B52/2002/Be | AY686489.2 | GIII.2 | |
| bovine/XJSHZ148/2011/CN | JQ905268.1 | GIII.2 | |
| BEC200/IT | HM745911.1 | GIII.2 | |
| Bo/Penrith55/00/UK | AY126476.1 | GIII.2 | |
| BEC830/IT | HM745913.1 | GIII.2 | |
| Bovine/ Wasme/B200/2003/Be | AY686494.1 | GIII.2 | |
| Bovine/Wasme/B199/2003/Be | AY686493.1 | GIII.2 | |
| CV186-OH | AF542084.1 | GIII.2 | |
| CV95-OH | AF542083.1 | GIII.2 | |
| Bo/ 21Z90/GIII.2/2012/Iran | KM650007.1 | GIII.2 | |
| BEC483/IT | HM745909.1 | GIII.2 | |
| Bovine/ Mohiville/B 123/2002/Be | AY686490.2 | GIII.2 | |
| Bo/4Z90/GIII.2/2012/Iran | KM650013.1 | GIII.2 | |
| Bo/6P90/GIII.2/2011/Iran | KM650011.1 | GIII.2 | |
| Bo/ 58B89/GIII.2/2010/Iran | KM650009.1 | GIII.2 | |
| Bo/27T90/GIII.2/2011/Iran | KM650012.1 | GIII.2 | |
| Bo/BEC/PenrithC39/2000/UK | DQ228162 | ||
| Bo/M3641/2000/HUN | JX018212 | ||
| bovine/ DijonA290-2/07/FR | GU259551 | ||
| bovine/DijonA386/08/FR | GU259561 | ||
| bovine/ DijonA364/08/FR | GU259556 | ||
| Bo/Nebraska/80/US | AY082891 | ||
| bovine/DijonA058/05/FR | GU259542 | ||
| Bo/BEC/Penrith140/2000/UK | DQ228159 | ||
| Bo/ BEC/Starcross93/2000/UK | DQ228165 | ||
| Nebovirus | Bo/CV548-OH/2002/US | AY549172 | |
| Bo/ CV531-OH/2002/US | AY549171 | ||
| Bo/ CV526-OH/2002/US | AY549170 | ||
| Bo/ CV504-OH/2002/US | AY549168 | ||
| Bo/ CV562-OH/2002/US | AY549173 | ||
| Bo/BEC/Starcross117/2000/UK | DQ228164 | ||
| Bo/BEC/Penrith142/2000/UK | DQ228160 | ||
| Bo/BEC/Penrith143/2000/UK | DQ228161 | ||
| Bo/ BEC/Penrith 150/2000/UK | DQ228157 | ||
| Bo/Newbury1/76/UK | NC_007916 | ||
| Bo/ DijonA216/06/FR | FJ687386 | ||
| BoNeV/ Sivas100/2016/TR | MG022086 | ||
| BoNeV/ Sivas120/2016/TR | MG022087 | ||
| BoNeV/ Sivas54/2016/TR | MG022088 | ||
| BoNeV/ Sivas60/2016/TR | MG022089 | ||
| BoNeV/ Sivas63/2016/TR | MG022090 | ||
| BoNeV/ Sivas64/2016/TR | MG022091 | ||
| BoNeV/ Sivas75/2016/TR | MG022092 |
Fig. 2
cladogram representing the phylogenic tree of bovine neboviruses based on 274 bp sequences. Each coloured branch indicates a different genotypes. Tree construction was built with use of Unipro UGENE v.1.21 software (14)
Fig. 3
Norovirus phylogenic tree constructed on 422 bp sequences. Alignment and classification of all genome data were performed by the UPGMA method with Unipro UGENE v. 1.21 software (14). Strains were coloured according to their genogroups. Novel norovirus sequences are shown as ruby red colour