Characterization of intra- and inter-host norovirus P2 genetic variability in linked individuals by amplicon sequencing

PLoS One. 2018 Aug 9;13(8):e0201850. doi: 10.1371/journal.pone.0201850. eCollection 2018.

Abstract

Noroviruses are the main cause of epidemics of acute gastroenteritis at a global scale. Although chronically infected immunocompromised individuals are regarded as potential reservoirs for the emergence of new viral variants, viral quasispecies distribution and evolution patterns in acute symptomatic and asymptomatic infections has not been extensively studied. Amplicons of 450 nts from the P2 coding capsid domain were studied using next-generation sequencing (454/GS-Junior) platform. Inter-host diversity between symptomatic and asymptomatic acutely infected individuals linked to the same outbreak as well as their viral intra-host diversity over time were characterized. With an average of 2848 reads per sample and a cutoff frequency of 0.1%, minor variant haplotypes were detected in 5 out of 8 specimens. Transmitted variants could not be confirmed in all infected individuals in one outbreak. The observed initial intra-host viral diversity in asymptomatically infected subjects was higher than in symptomatic ones. Viral quasispecies evolution over time within individuals was host-specific, with an average of 2.8 nt changes per day (0.0062 changes per nucleotide per day) in a given symptomatic case. Nucleotide polymorphisms were detected in 28 out of 450 analyzed nucleotide positions, 32.14% of which were synonymous and 67.86% were non-synonymous. Most observed amino acid changes emerged at or near blockade epitopes A, B, D and E. Our results suggest that acutely infected individuals, even in the absence of symptoms, which go underreported and may enhance transmission, may contribute to norovirus genetic variability and evolution.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Amino Acid Sequence
  • Caliciviridae Infections / epidemiology*
  • Caliciviridae Infections / virology*
  • Capsid Proteins / genetics*
  • Disease Outbreaks
  • Evolution, Molecular
  • Feces / virology
  • Genetic Variation*
  • Haplotypes
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Middle Aged
  • Models, Molecular
  • Norovirus / genetics*
  • Norovirus / isolation & purification
  • Nucleic Acid Amplification Techniques
  • Phylogeny
  • Viral Load

Substances

  • Capsid Proteins

Grants and funding

This work was supported in part by grants from the Fondo de Investigaciones Sanitarias Instituto de Salud Carlos III, Madrid, Spain [PS09/02516 (AD), PI 16/02005 (AD) and PI16/00337 (JQ]); https://portalfis.isciii.es], partially by the Spanish Ministry of Economy and Competitiveness (MINECO) [BIO2011-23461 (RMP); http://www.mineco.gob.es/], by the Centro para el Desarrollo Tecnológico Industrial-CDTI from MINECO [IDI-20151125 (JQ); https://www.cdti.es/], and by the XRB Biotechnology Reference Network (Generalitat de Catalunya) [(AB); http://www.xrb.cat]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors declare a commercial affiliation of JG with Roche Diagnostics S.L. which only provided support in the form of JG’s salary, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.