Molecular Characterization of Viruses from Clinical Respiratory Samples Producing Unidentified Cytopathic Effects in Cell Culture

Yacine Abed,Guy Boivin

doi:10.3390/v1020084

Abstract

The sequence-independent single primer amplification (SISPA) method was performed to identify a virus in 17 clinical respiratory samples producing uncharacterized cytopathic effects in LLC-MK2 cells. Sequence analysis of 600–1600 bp amplicons allowed the identification of six viruses (one influenza C, two parechovirus-3 and three cardioviruses). Genomic sequences of the cardioviruses showed similarities with those of the recently-described Saffold virus strain although significant variation was present in the viral surface EF and CD loops. These results demonstrate the usefulness of SISPA for identifying emerging viruses and also known viruses not easily identified by standard virological methods.

Highlights

Respiratory viral infections (RVIs) are a major cause of morbidity and mortality worldwide
Among the 17 clinical respiratory samples tested, the sequence-independent single primer amplication (SISPA) method allowed the identification of six viruses (Table 1)
The latter viruses originated from four nasophayngeal aspirates (NPA) and two bronchoalveolar lavages (BAL)

Summary

Introduction

Respiratory viral infections (RVIs) are a major cause of morbidity and mortality worldwide. An average of 7000 clinical samples are sent to the Regional Virology Laboratory of Québec City (Province of Québec, Canada) for viral identification using antigen detection tests, cellculture based techniques and PCR/RT-PCR assays. The aim of this study was to assess the ability of the sequence-independent single primer amplication (SISPA) method to identify some viruses producing uncharacterized CPE.

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Results

Conclusion