Genotyping Rotavirus RNA from Archived Rotavirus-Positive Rapid Test Strips

Lester M Shulman,Ilana Silberstein,Jacqueline Alfandari,Ella Mendelson

doi:10.3201/eid1701.101132

Lester M Shulman, Ilana Silberstein + Show 2 more

Open Access

https://doi.org/10.3201/eid1701.101132

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Abstract

Genotyping circulating rotaviruses before and after introduction of rotavirus vaccine is useful for evaluating vaccine-associated changes in genotype distribution. We determined frequency of rotavirus genotypes among 61 rotavirus-positive children hospitalized in Israel during the 2005–06 rotavirus season. Accurate molecular epidemiologic data were recovered from affinity-concentrated rotavirus immobilized in rotavirus-positive bands from air-dried, diagnostic rotavirus rapid test strips (dipstick) stored at room temperature from 1 week to 5 years. G genotypes were identical for 21 paired dipsticks and suspensions, whereas dipsticks or suspensions detected an additional G genotype in 2 samples. RNA sequences from 7 pairs were identical. Phylogenetic analysis suggested previously unreported G2 sublineages and G9 lineages. The ease with which dipsticks can be stored at local facilities and transported to central reference laboratories can reverse increasing difficulties in obtaining geographically representative stool samples and expand surveillance to regions lacking adequate laboratory facilities.

Highlights

Genotyping circulating rotaviruses before and after introduction of rotavirus vaccine is useful for evaluating vaccine-associated changes in genotype distribution
To assess the suitability of RNA extracted from dipsticks for determining the VP7 genotype, we first determined the VP7 G genotype of rotavirus in rotavirus-positive clinical samples from children hospitalized during May 15, 2005–May 15, 2006
Taking into account mixed infections, we found G1, G2, G3, and G9 G genotypes in 79%, 5%, 2%, and 15%, respectively, of the 62 rotaviruses identified in the 54 clinical samples

Summary

Introduction

Genotyping circulating rotaviruses before and after introduction of rotavirus vaccine is useful for evaluating vaccine-associated changes in genotype distribution. Accurate molecular epidemiologic data were recovered from affinity-concentrated rotavirus immobilized in rotavirus-positive bands from air-dried, diagnostic rotavirus rapid test strips (dipstick) stored at room temperature from 1 week to 5 years. The ease with which dipsticks can be stored at local facilities and transported to central reference laboratories can reverse increasing difficulties in obtaining geographically representative stool samples and expand surveillance to regions lacking adequate laboratory facilities. A colored band appears when indicator-linked rotavirus antibodies bind to the virus, and this complex is trapped on a band of membrane-bound rotavirus antibody on the dipstick With their growing use at point-of-care facilities and in local hospital laboratories, fewer samples are available for genotyping by centralized reference laboratories. Our main objective was to determine the feasibility of recovering molecular epidemiologic data from rotavirus immobilized on air-dried diagnostic rotavirus dipsticks to compensate for the decreasing number of fecal samples reaching central reference laboratories

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