Genetic recombination between two genotypes of genogroup III bovine noroviruses (BoNVs) and capsid sequence diversity among BoNVs and Nebraska-like bovine enteric caliciviruses

Abstract

To determine the genogroups and genotypes of bovine enteric caliciviruses (BECVs) circulating in calves, we determined the complete capsid gene sequences of 21 BECVs. The nucleotide and predicted amino acid sequences were compared phylogenetically with those of known human and animal enteric caliciviruses. Based on these analyses, 15 BECVs belonged to Norovirus genogroup III and genotype 2 (GIII/2) and were genetically distinct from human Norovirus GI and GII. Six BECVs had capsid gene sequences similar to that of the unclassified Nebraska (NB)-like BECV. The 15 bovine noroviruses (BoNVs) were more closely related to Bo/NLV/Newbury-2/76/UK (GIII/2) and other known genotype 2 BoNVs than to genotype 1 Bo/NLV/Jena/80/DE. The BoNV Bo/CV521-OH/02/US showed high nucleotide and amino acid identities (84 and 94%, respectively) with the capsid gene of Bo/NLV/Newbury-2/76/UK, whereas the nucleotide and amino acid sequences of the RNA polymerase gene were more closely related to those of Bo/NLV/Jena/80/DE (77 and 87% identities, respectively) than to those of Bo/NLV/Newbury-2/76/UK (69 and 69% identities, respectively), suggesting that Bo/CV521-OH/02/US is a genotype 1-2 recombinant. Gene conversion analysis by the recombinant identification program and SimPlot also predicted that Bo/CV521-OH/02/US was a recombinant. Six NB-like BECVs shared 88 to 92% nucleotide and 94 to 99.5% amino acid identities with the NB BECV in the capsid gene. The results of this study demonstrate genetic diversity in the capsid genes of BECVs circulating in Ohio veal calves, provide new data for coinfections with distinct BECV genotypes or genogroups, and describe the first natural BoNV genotype 1-2 recombinant, analogous to the previously reported human norovirus recombinants.

FIG. 1.

Phylogenetic tree, constructed by the neighbor-joining method, based on the amino acid sequence of the entire capsid gene of BoNV. The bootstrap value (percent) is given at each node. Viruses for which capsid gene sequences were used for phylogenetic analysis (GenBank accession numbers) included (i) GI human noroviruses Hu/NLV/Chiba407/87/JP (AB042808), Hu/NLV/Desert Shield395/90/SA (U04469), Hu/NLV/Hesse3/97/DE (AF093797), Hu/NLV/Musgrove/89/UK (AJ277614), Hu/NLV/Norwalk/68/US (M87661), Hu/NLV/Sindlesham/95/UK (AJ277615), Hu/NLV/Southampton/91/UK (L07418), and Hu/NLV/Winchester/94/UK (AJ277609); (ii) GII human noroviruses Hu/NLV/Bristol/93/UK (X76716), Hu/NLV/Camberwell1101922/94/AUS (AF145896), Hu/NLV/Hawaii/71/US (U07611), Hu/NLV/Hillingdon/90 (AJ277607), Hu/NLV/Leeds/90/UK (AJ277608), Hu/NLV/Lordsdale/93/UK (X86557), Hu/NLV/Melksham/89/UK (X81879), Hu/NLV/Mexico/89/MX (U22498), Hu/NLV/Seacroft/90/UK (AJ277620), Hu/NLV/Toronto24/91/CAN (U02030), Hu/NLV/Snow Mountain/76/US (U70059), and Hu/NLV/VA97207/97/US (AY038599); (iii) GII porcine noroviruses Sw/NLV/Sw43/97/JP (AB074892) and Sw/NLV/Sw918/97/JP (AB074893); and (iv) GIII bovine noroviruses: Bo/Aberystwyth24/00/UK (AY126475), Bo/CH126/98/NET (AF320625), Bo/CH131/98/NET (AF320113), Bo/CV95-OH/00/US (AF542083), Bo/CV186-OH/00/US (AF542084), Bo/Dumfries/94/UK (AY126474), Bo/Jena/80/DE (AJ011099), Bo/Newbury-2/76/UK (AF097917), and Bo/Penrith55/00/UK (AY126476).

FIG. 2.

Phylogenetic tree, constructed by the neighbor-joining method, based on the amino acid sequence of the entire capsid gene of NB-like BECV. The bootstrap value (percent) is given at each node. Viruses for which capsid gene sequences were used for phylogenetic analysis (GenBank accession numbers) included (i) GI human sapoviruses Hu/SLV/Houston/86/US (U95643), Hu/SLV/Houston/27/90/US (U95644), Hu/SLV/Manchester/93/UK (X86560), Lyon30388/98 (AJ251991), Hu/SLV/Parkville/94/US (U73124), Hu/SLV/Plymouth/92/UK (X86559), Hu/SLV/Sapporo/82/JP (U65427), and Hu/SLV/Stockholm/318/97/SE (AF194182); (ii) GII human sapoviruses Hu/SLV/Bristol/98/UK (AJ249939), Hu/SLV/cruise ship/00/US (AY289804), Hu/London/29845/92/UK (U95645), and Hu/SLV/Lyon/598/97/F (AJ271056); (iii) porcine sapovirus Sw/Cowden//UA (AF182760); (iv) mink sapovirus Canada 151A (AY144337); and (v) unclassified NB-like BECV Bo/NB/80/US (NC_004064).

FIG. 3.

Comparative phylogenetic trees, constructed by the unweighted-pair-group-method-with-arithmetic method, based on amino acid sequence of bovine noroviruses and representative human noroviruses. (A) S domain; (B) P2 domain. Bootstrap values of greater than 70% are given at each node.

FIG. 3.

Comparative phylogenetic trees, constructed by the unweighted-pair-group-method-with-arithmetic method, based on amino acid sequence of bovine noroviruses and representative human noroviruses. (A) S domain; (B) P2 domain. Bootstrap values of greater than 70% are given at each node.

FIG. 4.

Gene conversion analysis of Bo/CV521-OH/02/US compared with Bo/Jena/80/DE (black) and Bo/Newbury-2/76/UK (gray), using RIP (http://hivweb.lanl.gov/RIP/RIPsubmit.html). Program options were a window size of 100 and a threshold for statistical significance of 90%. The RdRp and capsid regions are indicated.