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禽流感:混合感染和缺失的病毒。

Avian influenza: mixed infections and missing viruses.

机构信息

Department of Pathology, Microbiology and Immunology, University of California, One Shields Avenue, Davis, CA 95616, USA.

出版信息

Viruses. 2013 Aug 5;5(8):1964-77. doi: 10.3390/v5081964.

Abstract

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.

摘要

在 2011 年夏天加利福尼亚州的野鸭种群中检测到高流行率和多样性的禽流感(AI)病毒,这为比较病毒培养前后的结果提供了机会。我们在培养前通过基质实时 PCR 以及扩增和测序血凝素(HA)基因的 640bp 部分来测试直肠拭子样本。每个样本还接种到鸡胚中,并确定培养病毒的全基因组序列。虽然低基质 Ct 值是从鸡蛋中分离病毒的良好预测指标,但 Ct 值高或不可检测的样本也产生了分离物。此外,鸡蛋中的单次传代改变了病毒株的出现和检测,并且培养后混合感染(不同的 HA 亚型)的检测频率降低。对于未知病毒的监测没有黄金标准或完美的参考比较,并且难以区分真正的阴性和假阴性。本研究表明,在培养前对样本进行测序可以增加混合感染的检测,并增强对病毒株和序列的鉴定,这些病毒株和序列在培养过程中可能已经发生变化甚至消失。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6ba1/3761236/66a9537b4c69/viruses-05-01964-g001.jpg

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