背景:季节性流感病毒(IVs)的局部传播可能难以解决。这里,我们研究了将血凝素(HA)和神经氨酸酶(NA)基因的高通量测序(HTS)与变异分析相结合是否可以从具有相同共有基因组的局部传播中分离菌株.我们分析了2020年1月在美国一所大型大学四天内收集的24个样本。我们扩增了完整的血凝素(HA)和神经氨酸酶(NA)基因组片段,然后进行Illumina测序。我们使用BLASTn鉴定了共有的完整HA和NA片段,并对HA和NA片段100%相似的菌株进行了变异分析。
结果:24个样本中有12个为PCR阳性,其中83.33%(10/12)通过从头组装检测到完整的HA和/或NA片段。相似性和系统发育分析表明,70%(7/10)的菌株是不同的,而其余30%的菌株具有相同的共有序列。这三个样品也具有IAV和IBV共感染。然而,随后的变异分析显示,它们具有不同的变异特征.虽然一个样本的IAVHA没有变异,另一个有T663C突变,另一个有C1379T和C1589A.
结论:在这项研究中,我们表明HTS与仅HA和NA基因的变异分析相结合可以帮助解决密切相关的变异。我们还提供证据表明,在2019-2020赛季的短时间内,IAV和IBV的共感染发生在大学校园,2020/2021和2021/2022世卫组织推荐的H1N1疫苗株都在共同传播。
BACKGROUND: Local transmission of seasonal influenza viruses (IVs) can be difficult to resolve. Here, we study if coupling high-throughput sequencing (HTS) of hemagglutinin (HA) and
neuraminidase (NA) genes with variant analysis can resolve strains from local transmission that have identical
consensus genome. We analyzed 24 samples collected over four days in January 2020 at a large university in the US. We amplified complete hemagglutinin (HA) and
neuraminidase (NA) genomic segments followed by Illumina sequencing. We identified
consensus complete HA and NA segments using BLASTn and performed variant analysis on strains whose HA and NA segments were 100% similar.
RESULTS: Twelve of the 24 samples were PCR positive, and we detected complete HA and/or NA segments by de novo assembly in 83.33% (10/12) of them. Similarity and phylogenetic analysis showed that 70% (7/10) of the strains were distinct while the remaining 30% had identical
consensus sequences. These three samples also had IAV and IBV co-infection. However, subsequent variant analysis showed that they had distinct variant profiles. While the IAV HA of one sample had no variant, another had a T663C mutation and another had both C1379T and C1589A.
CONCLUSIONS: In this study, we showed that HTS coupled with variant analysis of only HA and NA genes can help resolve variants that are closely related. We also provide evidence that during a short time period in the 2019-2020 season, co-infection of IAV and IBV occurred on the university campus and both 2020/2021 and 2021/2022 WHO recommended H1N1 vaccine strains were co-circulating.