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Norovirus in feces and nasopharyngeal swab of children with and without acute gastroenteritis symptoms: First report of GI.5 in Brazil and GI.3 in nasopharyngeal swab.

Author(s): Dábilla N, Nunes Vieira Almeida T, Carvalho Rebouças Oliveira A, Kipnis A, Neres Silva T, Souza Fiaccadori F, Teixeira de Sousa T, de Paula Cardoso DD, Souza M

Publication: J Clin Virol, 2017, Vol. 87, Page 60-66

PubMed ID: 28033513 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   This study compared the detection rates and viral loads of norovirus using a real-time qRT-PCR assay in fecal specimens and nasopharyngeal swab specimens from children. Fecal specimens and nasopharyngeal swab specimens were collected from May 2014 to May 2015 from 219 children between 0 and 70 months old (mean=15 months); 96 with acute gastroenteritis symptoms (diarrhea with or with-out vomiting and/or fever) and 123 children without symptoms. Details for specimen collection were not provided. Specimens were stored at 4°C until transport to a regional laboratory. Nasopharyngeal swab specimens were homogenized by vortexing, swabs were removed, tubes were centrifuged at 1300 × g at 10°C for 10 min, and supernatants stored at -80°C. Fecal suspensions were prepared using phosphate-buffered saline and stored at -80°C. RNA was extracted from all specimens using the QIAamp Viral RNA Minikit. Noroviruses were detected using the GI/GII NoV Duplex real-time RT-PCR assay. To determine genotypes, specimens with the highest viral loads were subjected to conventional RT-PCR assays using the same primer pair used in the RT-qPCR assay and sequenced by an automated sequencer.

   Summary of Findings:

   Positivity rates for norovirus were comparable between asymptomatic and symptomatic patients in fecal specimens (15.4% and 18.8%, respectively) and nasopharyngeal swab specimens (6.5% and 11.4%, respectively). Similarly, median viral loads were comparable among asymptomatic and symptomatic patients in both fecal specimens (4.32 × 107 GC/g and 2.69 × 108 GC/g, respectively) and nasopharyngeal specimens (1.73 × 106 GC/mL and 2.20 × 107 GC/mL, respectively). Norovirus was detected in both the fecal specimen and nasopharyngeal swab of the same patient in only two cases (one symptomatic and one asymptomatic). Sequencing of norovirus-positive specimens with the highest viral loads identified six genotypes in the 14 fecal specimens selected: GII.4 (35.7%), GII.6 (21.4%), GI.3 (14.4%), GII.3 (14.4%), GI.2 (7.1%), and GI.5 (7.1%) but only GI.3 was detected in the two nasopharyngeal specimens selected.

   Biospecimens

   • Cell - Nasopharynx
   • Bodily Fluid - Feces

   Preservative Types

   • Frozen

   Diagnoses:

   • Pneumonia/Respiratory Infection

   Platform:

   Analyte	Technology Platform
   RNA	Real-time qRT-PCR
   RNA	RT-PCR
   RNA	DNA sequencing

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Biospecimen location	Nasopharynx Feces
   RT-PCR Specific	Targeted nucleic acid	Norovirus GI Norovirus GII
   Real-time qRT-PCR Specific	Targeted nucleic acid	Norovirus GI Norovirus GII

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