Strategy for efficient generation of numerous full-length cDNA clones of classical swine fever virus for haplotyping.
BMC Genomics
; 19(1): 600, 2018 Aug 09.
Article
en En
| MEDLINE
| ID: mdl-30092775
ABSTRACT
BACKGROUND:
Direct molecular cloning of full-length cDNAs derived from viral RNA is an approach to identify the individual viral genomes within a virus population. This enables characterization of distinct viral haplotypes present during infection.RESULTS:
In this study, we recover individual genomes of classical swine fever virus (CSFV), present in a pig infected with vKos that was rescued from a cDNA clone corresponding to the highly virulent CSFV Koslov strain. Full-length cDNA amplicons (ca. 12.3 kb) were made by long RT-PCR, using RNA extracted from serum, and inserted directly into a cloning vector prior to detailed characterization of the individual viral genome sequences. The amplicons used for cloning were deep sequenced, which revealed low level sequence variation (< 5%) scattered across the genome consistent with the clone-derived origin of vKos. Numerous full-length cDNA clones were generated using these amplicons and full-genome sequencing of individual cDNA clones revealed insights into the virus diversity and the haplotypes present during infection. Most cDNA clones were unique, containing several single-nucleotide polymorphisms, and phylogenetic reconstruction revealed a low degree of order.CONCLUSIONS:
This optimized methodology enables highly efficient construction of full-length cDNA clones corresponding to individual viral genomes present within RNA virus populations.Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Haplotipos
/
ARN Viral
/
Técnicas Genéticas
/
ADN Complementario
/
Peste Porcina Clásica
/
Virus de la Fiebre Porcina Clásica
Tipo de estudio:
Prognostic_studies
Límite:
Animals
Idioma:
En
Revista:
BMC Genomics
Asunto de la revista:
GENETICA
Año:
2018
Tipo del documento:
Article
País de afiliación:
Dinamarca