Novel GII.12 norovirus strain, United States, 2009-2010

Abstract

In October 2009, a novel GII.12 norovirus strain emerged in the United States and caused 16% of all reported norovirus outbreaks during the winter season. Sequence analysis demonstrated a recombinant virus with a P2 region that was largely conserved compared with previously sequenced GII.12 strains.

Figure 1

Phylogenetic trees of the P2 region in open reading frame (ORF) 2 and region A in ORF1 of noroviruses, United States. The P2 region and region A phylogenetic trees include GII.12 sequences from strains submitted to GenBank and GII.12 sequences reported in this study. In addition, region A analysis includes GII.12 Pune (GenBank accession no. EU921353), GII.1 (accession no. U07611), and GII.13 (accession no. DQ379714) sequences. Branch identifiers for the P2 region are as follows, with GenBank accession numbers in parentheses: A) Pune (EU921353); B) Pirna (AF427119); C) Wortley (AJ277618); H) Akabane (EF547403), Hiroshima (AB044366), Chitta virus (AB032758), Honolulu (AF414420), Gifu’96 (AB045603), U1GII (AB067536), U1 (AB039775), and Schwerin (AF397905). The GII.12 phylogenetic tree of the P2 region and region A region include GII.12 sequences StGeorge (accession no. GQ845370), Shelby (accession no. HQ688986), and all GII.12 noroviruses from 2009 through June 2010 (not distinguishable from GII.12 2009–10 cluster). The P2 region analysis also includes the Velence strain (accession no. HQ115742). Scale bars indicate nucleotide substitutions per site.

Figure 2

GII.12 norovirus viral protein (VP) 1 cartoon depicting amino acid similarities and locations between 2009–10 GII.12 strains and pre-2009 GII.12 strains. The S, P1, and P2 domains of VP1 are labeled accordingly. The VP1 amino acid numbering is based on the GII.12 prototype strain Wortley (GenBank accession no. AJ277618). Amino acid types are indicated by colors: green, polar; blue, basic; red, acidic; and black, hydrophobic. The 80% consensus sequence is based on a VP1 consensus sequence from the following GII.12 strains: GenBank accession nos. EU921353, AF427119, AJ277618, EF547403, AB044366, AB032758, AF414420, AB045603, AB067536, AB039775, and AF397905. Three recombinant 2009–2010 GII.12 strains—StGeorge (accession no. GQ845370), Velence (accession no. HQ115742), and Shelby (accession no. HQ688986)—were not included. The Centers for Disease Control and Prevention (CDC)–80% consensus–2009v and CDC–80% consensus–pre-2009 sequences are based on an 80% consensus P2 sequence from samples received from 2009–2010 (2009v) or from sample before 2009 (pre-2009), respectively.

Figure A1

Number of GII.12 norovirus outbreaks reported to the Centers for Disease Control and Prevention November 2007–June 2010.