Journal
INFECTION GENETICS AND EVOLUTION
Volume 20, Issue -, Pages 276-283Publisher
ELSEVIER
DOI: 10.1016/j.meegid.2013.09.007
Keywords
Rotavirus Wa; Sequence-independent genome amplification; Consensus sequence; Phylogenetic analysis; Molecular clock analysis; Genome segment rearrangement
Categories
Funding
- European Foundation Initiative for Neglected Tropical Diseases (EFINTD) [I/84 015]
- Poliomyelitis Research Foundation, South Africa [09/41]
- National Research Foundation, South Africa
Ask authors/readers for more resources
The consensus nucleotide sequence of a human rotavirus Wa strain, with only a partially known passage history, was determined with sequence-independent amplification and next generation 454 (R) pyrosequencing. This rotavirus Wa strain had the expected genome constellation of G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and was designated RVA/Human-tc/USA/WaCS/1974/G1P[8]. Phylogenetic analyses revealed a close relationship to four human rotavirus Wa variants (Wag5re, Wag7/8re, ParWa and VirWa) derived from the original 1974 human isolate. There were rearrangements in the Wag5re- and Wag7/8re variants in genome segments 5 (Wag5re) and 7 and 8 (Wag7/8re), which were not present in WaCS. Pairwise comparisons and a combined molecular clock for the Wa rotavirus genome indicated a close relationship between WaCS and ParWa and VirWa. These results suggest that WaCS is most probably an early cell culture adapted variant from the initial gnotobiotic pig passaged Wa isolate. Evolutionary pressure analysis identified a possible negative selected amino acid site in VP1 (genome segment 1) and a likely positive selected site in VP4 (genome segment 4). The WaCS may be more appropriate as a rotavirus Wa reference sequence than the current composite Wa reference genome. (C) 2013 Elsevier B. V. All rights reserved.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available