Complete Genome Sequence of a Nontypeable GII Norovirus Detected in Peru.

Norovirus, a leading cause of acute gastroenteritis in humans, is a highly diverse virus. Here, we report the complete genome sequence of a nontypeable genogroup II (GII) norovirus that was detected in a symptomatic Peruvian child in 2008. This virus showed low nucleotide sequence identities (≤82%) against all known genotypes.

GENOME ANNOUNCEMENT

Norovirus is an important cause of acute gastroenteritis. Based on the sequence differences of the major capsid protein (VP1), norovirus is currently divided into seven genogroups (GI to GVII) and more than 30 genotypes (1). Because of the sequence diversity of the RNA-dependent RNA polymerase (RdRp), norovirus typing is based on a dual classification system, which includes polymerase and capsid genotypes (2).

Here, we report the complete genome sequence of a nontypeable GII strain. This strain was detected in a stool sample (PNV06929) collected in 2008 from an 8-month-old Peruvian child with diarrhea (3). The viral RNA was extracted from a 10% stool suspension using the MagMAX viral RNA isolation kit (Ambion, CA), and the full-length norovirus genome was amplified by reverse transcription-PCR, as described by Parra et al. (4). The approximately 7.5-kb PCR product was gel purified using the QIAquick gel extraction kit (Qiagen, CA) and subjected to next-generation sequencing (NGS). The library for NGS was prepared using the Nextera XT DNA library prep kit (Illumina, CA), and the paired-end 2 × 250-bp reads were obtained using the MiSeq system (Illumina). Reads were quality filtered (base quality score, ≥ 20) and mapped against the reference genomes (Hu/PE/2013/GII.P24-GII.24/Loreto1972, GenBank accession number KY225989; and YURI, GenBank accession number AB083780) to reconstruct a consensus sequence using the HIVE-hexagon (5). A total of 635,163 reads were obtained, covering 7,465 nucleotides (nt) of the viral genome, with an average depth of coverage of 16,664× (range, 230 to 23,398×). The nucleotide sequences of the 5ʹ untranslated region (UTR) and 3ʹ UTR of the viral genome were obtained using Sanger sequencing and the 5ʹ/3ʹ rapid amplification of cDNA ends (RACE) kit (Sigma-Aldrich, MO).

The complete genome of this virus, excluding the poly(A) tail, was 7,525 nt in length and presented three open reading frames (ORFs), ORF1, ORF2, and ORF3, which were 5,091, 1,629, and 765 nt in length, respectively. ORF1 encodes a polyprotein that is cleaved into 6 nonstructural proteins (NS) spanning the sequence as follows: nt 5 to 1000, NS1/2 (p48); nt 1001 to 2098, NS3 (NTPase); nt 2099 to 2620, NS4 (p22); nt 2621 to 3019, NS5 (VPg); nt 3020 to 3562, NS6 (3C-like protease); and nt 3563 to 5095, NS7 (RdRp). The length of the 5ʹ UTR was 4 nt, and that of the 3ʹ UTR was 57 nt, excluding the poly(A) tail. Sequence analyses indicated that the closest strains were GII.P24-GII.24 (Hu/PE/2013/GII.P24-GII.24/Loreto1972; Hu/US/2013/GII.P24-GII.24/EdenPrairie5457, GenBank accession number MG495084; Hu/US/2013/GII.P24-GII.24/EdenPrairie5458, GenBank accession number MG495085) and unassigned strains GII.PNA1-GII.NA1 (Hu/PE/2012/GII.PNA1-GII.NA1/Loreto0959, GenBank accession number MG495077; Hu/PE/2012/GII.PNA1-GII.NA1/Loreto1041, GenBank accession number MG495078) and GII.PNA3-GII.NA3 (Hu/NI/2005/GII.PNA3-GII.NA3/Leon4509, GenBank accession number KU306738) as of 2 January 2018; all presented ≤82% nt identity using full-length genome sequences. Phylogenetic analysis of the VP1-encoding sequence was done using MEGA7 (6) and showed no clustering of this virus with any of the GII.24, GII.NA1, or GII.NA3 strains. The RdRp-encoding region of this virus also did not cluster with any known strains. The differences presented with other characterized noroviruses suggest that this virus could form a novel GII genotype. Additional studies conducted in different locations are required to confirm that this could be a new genotype.

Accession number(s).

The complete genome sequence of this strain (Hu/GII/PNV06929/2008/PER) has been deposited in GenBank under the accession number MG706448.