Effect of oligonucleotide primers in determining viral variability within hosts.docVIP

Virology Journal BioMedCentral Methodology Open Access Effect of oligonucleotide primers in determining viral variability within hosts Maria Alma Bracho*?, Inmaculada García-Robles?, Nuria Jiménez, Manuela Torres-Puente, Andrés Moya and Fernando González-Candelas Address: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Edifici Instituts, Polígon La Coma s/n, Paterna (València) 46980 SPAIN Email: Maria Alma Bracho* - alma.bracho@uv.es; Inmaculada García-Robles - inmaculada.garcia@uv.es; Nuria Jiménez - nuria.jimenez@uv.es; Manuela Torres-Puente - manoli.torres@uv.es; Andrés Moya - andres.moya@uv.es; Fernando González-Candelas - fernando.gonzalez@uv.es * Corresponding author ?Equal contributors Published: 09 December 2004 Received: 22 October 2004 Accepted: 09 December 2004 Virology Journal 2004, 1:13 doi:10.1186/1743-422X-1-13 This article is available from: /content/1/1/13 ? 2004 Bracho et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR) based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet. Results: To investigate the role of oligonucleotide design in estimating viral variability within hosts, genetic diversity in hepatitis C virus (HCV) populations from eight infected patients was characterised by two parallel PCR amplifications perfo