Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA.
School of Informatics Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, USA.
mBio. 2019 Jan 22;10(1):e02262-18. doi: 10.1128/mBio.02262-18.
Enteroviruses are a common cause of respiratory and gastrointestinal illness, and multiple subtypes, including poliovirus, can cause neurologic disease. In recent years, enterovirus D68 (EV-D68) has been associated with serious neurologic illnesses, including acute flaccid myelitis (AFM), frequently preceded by respiratory disease. A cluster of 11 suspect cases of pediatric AFM was identified in September 2016 in Phoenix, AZ. To determine if these cases were associated with EV-D68, we performed multiple genomic analyses of nasopharyngeal (NP) swabs and cerebrospinal fluid (CSF) material from the patients, including real-time PCR and amplicon sequencing targeting the EV-D68 VP1 gene and unbiased microbiome and metagenomic sequencing. Four of the 11 patients were classified as confirmed cases of AFM, and an additional case was classified as probable AFM. Real-time PCR and amplicon sequencing detected EV-D68 virus RNA in the three AFM patients from which NP swabs were collected, as well as in a fourth patient diagnosed with acute disseminated encephalomyelitis, a disease that commonly follows bacterial or viral infections, including enterovirus. No other obvious etiological causes for AFM were identified by 16S or RNA and DNA metagenomic sequencing in these cases, strengthening the likelihood that EV-D68 is an etiological factor. Herpes simplex viral DNA was detected in the CSF of the fourth case of AFM and in one additional suspect case from the cluster. Multiple genomic techniques, such as those described here, can be used to diagnose patients with suspected EV-D68 respiratory illness, to aid in AFM diagnosis, and for future EV-D68 surveillance and epidemiology. Enteroviruses frequently result in respiratory and gastrointestinal illness; however, multiple subtypes, including poliovirus, can cause severe neurologic disease. Recent biennial increases (i.e., 2014, 2016, and 2018) in cases of non-polio acute flaccid paralysis have led to speculations that other enteroviruses, specifically enterovirus D68 (EV-D68), are emerging to fill the niche that was left from poliovirus eradication. A cluster of 11 suspect cases of pediatric acute flaccid myelitis (AFM) was identified in 2016 in Phoenix, AZ. Multiple genomic analyses identified the presence of EV-D68 in the majority of clinical AFM cases. Beyond limited detection of herpesvirus, no other likely etiologies were found in the cluster. These findings strengthen the likelihood that EV-D68 is a cause of AFM and show that the rapid molecular assays developed for this study are useful for investigations of AFM and EV-D68.
肠道病毒是引起呼吸道和胃肠道疾病的常见原因，多种亚型，包括脊髓灰质炎病毒，可引起神经系统疾病。近年来，肠道病毒 D68（EV-D68）与严重的神经系统疾病有关，包括急性弛缓性脊髓炎（AFM），通常先有呼吸道疾病。2016 年 9 月，亚利桑那州凤凰城发现了 11 例疑似儿科 AFM 的病例。为了确定这些病例是否与 EV-D68 有关，我们对患者的鼻咽（NP）拭子和脑脊液（CSF）样本进行了多种基因组分析，包括针对 EV-D68 VP1 基因的实时 PCR 和扩增子测序，以及无偏微生物组和宏基因组测序。11 例患者中有 4 例被归类为确诊的 AFM 病例，另有 1 例被归类为可能的 AFM 病例。从采集 NP 拭子的 3 例 AFM 患者以及另外 1 例诊断为急性播散性脑脊髓炎的患者中，实时 PCR 和扩增子测序均检测到 EV-D68 病毒 RNA，急性播散性脑脊髓炎是一种常见于细菌或病毒感染（包括肠道病毒）后的疾病。在这些病例中，16S 或 RNA 和 DNA 宏基因组测序未发现其他明显的 AFM 病因，这进一步证实了 EV-D68 是病因的可能性。在第四例 AFM 患者的 CSF 中检测到单纯疱疹病毒 DNA，在该群组的另一个疑似病例中也检测到了单纯疱疹病毒 DNA。这里描述的多种基因组技术可用于诊断疑似 EV-D68 呼吸道疾病的患者，辅助 AFM 诊断，并用于未来的 EV-D68 监测和流行病学研究。肠道病毒常引起呼吸道和胃肠道疾病；然而，多种亚型，包括脊髓灰质炎病毒，可导致严重的神经系统疾病。近年来，非脊髓灰质炎急性弛缓性麻痹病例每两年增加一次（即 2014 年、2016 年和 2018 年），这导致人们猜测，其他肠道病毒，特别是肠道病毒 D68（EV-D68），正在出现，以填补脊髓灰质炎病毒根除后留下的空白。2016 年，亚利桑那州凤凰城发现了 11 例疑似儿科急性弛缓性脊髓炎（AFM）的病例。多项基因组分析发现，大多数临床 AFM 病例中存在 EV-D68。在该群组中，除了有限的疱疹病毒检测外，没有发现其他可能的病因。这些发现进一步证实了 EV-D68 是 AFM 的病因，并表明本研究中开发的快速分子检测方法可用于 AFM 和 EV-D68 的研究。
