Molecular characterization of Camberwell virus and sequence variation in ORF3 of small round‐structured (Norwalk‐like) viruses

Abstract

Five small round-structured viruses (SRSVs) associated with gastroenteritis in Victoria, Australia, from January to November 1994 were examined by sequencing cDNA prepared from faecal samples using RT-PCR. The sequence of the 3' half (3.8 kb) of the genome of one of these viruses, Camberwell, was determined. Camberwell virus was related most closely to Bristol and Lordsdale viruses, and belonged to the genetic group of SRSVs containing Bristol, Lordsdale, Toronto, OTH-25, Mexico, and Hawaii viruses. The amino acid identities between Camberwell and Bristol viruses for proteins encoded by ORF1 (partial), ORF2, and ORF3 were 99%, 98%, and 90%, respectively. A highly variable region in ORF3 corresponding to amino acid residues 123 to 169 (Bristol and Camberwell numbering) were identified. Short segments of ORF1 (polymerase region) and the highly variable ORF3 region was analysed for the other four viruses. The results obtained indicated the potential usefulness of the variable region in distinguishing between closely related viruses.

Genetic classification of "Sapporo-like viruses"

“…Overall, both the separate and combined alignments of the SLV and NLV sequences showed relatively good concordance with those previously reported [3,13,16,18,27,35,42]. However, the alignment of 10 SLV sequences indicated marked differences in the amino acid and nucleotide sequences of the 3 end of the 3 ORF and the 5 end of the 3 UTR of London/92 strain compared to the remaining 9 SLV strains.…”

“…In addition, in all published SLV strains except a human strain, London/92 and a porcine strain, PEC/Cowden [5,15,18,27,29,40], an additional ORF has been predicted in +1 frame, overlapping the N terminus of the capsid gene (capsid overlap). To date, the sequence of a ∼3-kb region extending from the RNA polymerase gene to the 3 poly(A) tail is available in GenBank for 9 NLV strains, of which 6 have had their entire genome sequenced: Norwalk/68 [17], Southampton/91 [22], Lordsdale/93 [9], Camberwell/94 [3,36], Chiba/87 (GenBank accession number No. AB042808) and Jena/80 [26].…”

Covariation of Major and Minor Viral Capsid Proteins in Norovirus Genogroup II Genotype 4 Strains

“…In this study, we found sequence hypervariability in the P2 domain of VP1 and, more importantly, in the VP1 interaction domain of VP2 in NoV GII.4 lineage on 3 levels: (i) in the global evolution of pandemic/epidemic strains from the mid-1970s through post-2006, (ii) in the local emergence of an epidemic strain, and (iii) in an immunocompromised patient chronically shedding NoV. Our findings agree with observations in earlier work that the VP2 gene is highly variable (based on multiple sequence alignment) (2,4,14). It is noteworthy that our findings from scanning nucleotide analysis establish the link between VP2 sequence hypervariability and the putative VP1 interaction domain, hinting at coevolution of VP1 and VP2.…”

Characterization of Monoclonal Antibodies Generated against Norwalk virus Gil Capsid Protein Expressed in Escherichia coli

“…PCR consisted of 30 cycles of denaturation (94 C for 30 sec), primer annealing (55 C for 30 sec) and extension (72 C for 30 sec). Both strands of the products were sequenced using the PRISM' Dye-Deoxy Terminator Cycle Sequencing Kit (Perkin Elmer ABI, U.S.A.) with the same primers used for PCR as described by Cauchi et al (1) and analyzed using the 310 Genetic Analyzer (Perkin Elmer ABI). Production and partial purification of recombinant proteins.…”