Sammanfattning

This study describes the design of degenerate primers and their use for synthesis of full-length avian influenza A neuramindase (NA). Each reaction was performed using either two forward primers and one reverse primer, or one forward primer and one reverse primer. Both primer combinations had comparable amplification efficiencies for all NA subtypes (1-9). A total of 11 virus strains, including both field isolates and reference strains, were amplified successfully using these degenerate primer sets. Of the sequences amplified, 108 strains (93.9%) resulted in near full-length NA cDNAs after two readings with one forward primer and one reverse primer. Of the remaining sequences, five strains (4.3%) yielded reads with enough information for subtype categorization by BLAST although they were of insufficient quality for assembly. One strain (0.9%) yielded different subtypes from both sequence reads whereas the other one (0.9%) was not possible to assemble and subtype. This successful demonstration of these degenerate primers for the amplification and sequencing of all avian NA subtypes suggests that these primers could be employed in the avian influenza surveillance program as well as studies of antiviral resistance, virus ecology or viral phylogeny. (C) 2010 Elsevier B.V. All rights reserved.

Nyckelord

Influenza A virus; Neuraminidase; Sequencing; PCR; Degenerate primers

Publicerad i

Journal of Virological Methods
2010, Volym: 170, nummer: 1-2, sidor: 94-98
Utgivare: ELSEVIER SCIENCE BV

SLU författare

• Muradrasoli, Shaman

  • Institutionen för husdjurens biovetenskaper, Sveriges lantbruksuniversitet
    

Associerade SLU-program

AMR: Virus


UKÄ forskningsämne

Biokemi och molekylärbiologi


Publikationens identifierare

DOI: https://doi.org/10.1016/j.jviromet.2010.09.006

Permanent länk till denna sida (URI)

https://res.slu.se/id/publ/47758