Tweet
J Clin Virol. 2015 Jul;68:16-23. doi: 10.1016/j.jcv.2015.04.010. Epub 2015 Apr 11.
Viral subpopulation diversity in influenza virus isolates compared to clinical specimens.
Rutvisuttinunt W1, Chinnawirotpisan P2, Thaisomboonsuk B3, Rodpradit P4, Ajariyakhajorn C5, Manasatienkij W6, Simasathien S7, Shrestha SK8, Yoon IK9, Klungthong C10, Fernandez S11.
Author information
Abstract
BACKGROUND:
Influenza virus (IFV) isolates obtained from mammalian cell cultures are valuable reagents used for vaccine production, antigenic characterization, laboratory assays, and epidemiological and evolutionary studies. Complete genomic comparison of IFV isolates with their original clinical specimens provides insight into cell culture-driven genomic changes which may sequentially alter the virus phenotype.
OBJECTIVES:
The genome of the viral isolates and of the viruses in the clinical specimens was examined by deep sequencing in order to determine nucleotide heterogeneity (measured number of variances or numbers of mixed bases) as a marker for IFV population diversity.
STUDY DESIGN:
Clinical respiratory specimens were collected between July and October 2012 and identified by RT-PCR as positive for influenza A H3N2 or H1N1, or influenza B. The viruses in the clinical specimens were amplified using mammalian cell culture. Next generation sequencing (NGS) was used to investigate genomic differences between IFV isolates and their corresponding clinical specimens.
RESULTS:
There was less nucleotide heterogeneity in 5 of 6 viral isolates compared to the corresponding clinical specimens, especially for influenza B. A phylogenetic analysis of the hemagglutinin (HA) gene consensus sequences obtained from deep and Sanger sequencing showed that the viral isolates and their corresponding clinical specimens contained the same IFV strains with less than 5% pair-wise genetic distance.
CONCLUSION:
The IFV sequence data analysis detected a substantial decrease in nucleotide heterogeneity from clinical specimens to viral cultures in 5 out of 6 investigated cases.
Copyright ? 2015 The Authors. Published by Elsevier B.V. All rights reserved.
KEYWORDS:
Clinical specimens; Influenza; Next generation Sequencing; Variances; Viral isolates; Viral subpopulations
PMID: 26071329 [PubMed - in process] Free full text
Viral subpopulation diversity in influenza virus isolates compared to clinical specimens.
Rutvisuttinunt W1, Chinnawirotpisan P2, Thaisomboonsuk B3, Rodpradit P4, Ajariyakhajorn C5, Manasatienkij W6, Simasathien S7, Shrestha SK8, Yoon IK9, Klungthong C10, Fernandez S11.
Author information
Abstract
BACKGROUND:
Influenza virus (IFV) isolates obtained from mammalian cell cultures are valuable reagents used for vaccine production, antigenic characterization, laboratory assays, and epidemiological and evolutionary studies. Complete genomic comparison of IFV isolates with their original clinical specimens provides insight into cell culture-driven genomic changes which may sequentially alter the virus phenotype.
OBJECTIVES:
The genome of the viral isolates and of the viruses in the clinical specimens was examined by deep sequencing in order to determine nucleotide heterogeneity (measured number of variances or numbers of mixed bases) as a marker for IFV population diversity.
STUDY DESIGN:
Clinical respiratory specimens were collected between July and October 2012 and identified by RT-PCR as positive for influenza A H3N2 or H1N1, or influenza B. The viruses in the clinical specimens were amplified using mammalian cell culture. Next generation sequencing (NGS) was used to investigate genomic differences between IFV isolates and their corresponding clinical specimens.
RESULTS:
There was less nucleotide heterogeneity in 5 of 6 viral isolates compared to the corresponding clinical specimens, especially for influenza B. A phylogenetic analysis of the hemagglutinin (HA) gene consensus sequences obtained from deep and Sanger sequencing showed that the viral isolates and their corresponding clinical specimens contained the same IFV strains with less than 5% pair-wise genetic distance.
CONCLUSION:
The IFV sequence data analysis detected a substantial decrease in nucleotide heterogeneity from clinical specimens to viral cultures in 5 out of 6 investigated cases.
Copyright ? 2015 The Authors. Published by Elsevier B.V. All rights reserved.
KEYWORDS:
Clinical specimens; Influenza; Next generation Sequencing; Variances; Viral isolates; Viral subpopulations
PMID: 26071329 [PubMed - in process] Free full text