Rotavirus Strain Trends in United States, 2009-2016: Results from the National Rotavirus Strain Surveillance System (NRSSS)

Abstract

Before the introduction of vaccines, group A rotaviruses (RVA) were the leading cause of acute gastroenteritis in children worldwide. The National Rotavirus Strain Surveillance System (NRSSS) was established in 1996 by the Centers for Disease Control and Prevention (CDC) to perform passive RVA surveillance in the USA. We report the distribution of RVA genotypes collected through NRSSS during the 2009-2016 RVA seasons and retrospectively examine the genotypes detected through the NRSSS since 1996. During the 2009-2016 RVA seasons, 2134 RVA-positive fecal specimens were sent to the CDC for analysis of the VP7 and VP4 genes by RT-PCR genotyping assays and sequencing. During 2009-2011, RVA genotype G3P[8] dominated, while G12P[8] was the dominant genotype during 2012-2016. Vaccine strains were detected in 1.7% of specimens and uncommon/unusual strains, including equine-like G3P[8] strains, were found in 1.9%. Phylogenetic analyses showed limited VP7 and VP4 sequence variation within the common genotypes with 1-3 alleles/lineages identified per genotype. A review of 20 years of NRSSS surveillance showed two changes in genotype dominance, from G1P[8] to G3P[8] and then G3P[8] to G12P[8]. A better understanding of the long-term effects of vaccine use on epidemiological and evolutionary dynamics of circulating RVA strains requires continued surveillance.

Keywords: RVA; genotype; prevalence; rotavirus; surveillance; vaccine.

Figure 1

Phylogenetic trees based on aligned nucleotide sequences of the VP7 (585 nt) and VP4 (537 nt) genes of RVAs. Sequence alignments were generated for each genotype using MUSCLE. Top BLAST hits along with lineage reference sequences were also included in these alignments. Optimal models were selected using jModeltest2 using the corrected Aikaike information criterion (AICc). Maximum likelihood trees were generated using PhyML using the approximate likelihood-ratio test (aLRT) option for branch support (see Supplementary Material for aLRT values). Genotype-specific sub lineages are color-coded; genotypes, lineages, and alleles are indicated. Scale bars indicate the number of nucleotide substitutions per site.

Figure 2

The percent distribution of six major genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]) during the 1997–2016 seasons; data from 1997 through 2008 seasons were obtained from previously published reports. Rarer genotypes were not accounted for in this graphical representation. Percentages were calculated using samples which tested positive by EIA at the collection site and were confirmed at the CDC. Percentage of common genotypes was adjusted to equal 100% per season. Several co-dominant genotypes were detected at comparable levels during the 2011 and 2012 RV seasons, denoted on the graph with a gray dashed box. The licensure year of each RVA vaccine is denoted by the black dashed vertical lines.