Avian influenza: mixed infections and missing viruses.
A high prevalence and diversity of avian influenza (AI) viruses were detected in a population of wild mallards sampled during summer 2011 in California, providing an opportunity to compare results obtained before and after virus culture. We tested cloacal swab samples prior to culture by matrix real-time PCR, and by amplifying and sequencing a 640bp portion of the hemagglutinin (HA) gene. Each sample was also inoculated into embryonated chicken eggs, and full genome sequences were determined for cultured viruses. While low matrix Ct values were a good predictor of virus isolation from eggs, samples with high or undetectable Ct values also yielded isolates. Furthermore, a single passage in eggs altered the occurrence and detection of viral strains, and mixed infections (different HA subtypes) were detected less frequently after culture. There is no gold standard or perfect reference comparison for surveillance of unknown viruses, and true negatives are difficult to distinguish from false negatives. This study showed that sequencing samples prior to culture increases the detection of mixed infections and enhances the identification of viral strains and sequences that may have changed or even disappeared during culture.
Department of Pathology, Microbiology and Immunology, University of California, One Shields Avenue, Davis, CA 95616, USA. lllindsay@ucdavis.edu
LeAnn L
LL
Lindsay
Terra R
TR
Kelly
Magdalena
M
Plancarte
Seth
S
Schobel
Xudong
X
Lin
Vivien G
VG
Dugan
David E
DE
Wentworth
Walter M
WM
Boyce
D000818:Animals; D046090:Anseriformes / Q000821:virology*; D002140:California / Q000453:epidemiology; D002645:Chickens; D002988:Cloaca / Q000821:virology; D060085:Coinfection / Q000821:virology*; D062665:Epidemiological Monitoring; D005260:Female; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D009980:Influenza A virus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000821:virology*; D008297:Male; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA; D014773:Virology / Q000379:methods*; D014776:Virus Cultivation / Q000379:methods
D019267:Hemagglutinin Glycoproteins, Influenza Virus; D012367:RNA, Viral