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Genetic analysis of Enterovirus D68 associated with pneumonia in children from South India
Journal of Medical Microbiology ( IF 3 ) Pub Date : 2021-05-17 , DOI: 10.1099/jmm.0.001356
Ramachandran Erathodi Sanjay 1 , Sasidharanpillai Sabeena 1 , Sudandiradas Robin 1 , John T Shaji 2 , M P Jayakrishnan 3 , E K Kumar Suresh 4 , C J Michael 5 , S Aswathyraj 1 , Joseph Josmi 1 , Sheik Shahin 1 , Jayaram Anup 1 , Govindakarnavar Arunkumar 1, 6
Affiliation  

EV-D68 is an emerging enterovirus infection associated with severe acute respiratory illness (SARI), acute flaccid myelitis (AFM) and acute flaccid paralysis (AFP). While EV-D68 outbreaks and sporadic cases are reported globally, a single case has been reported from India. The present study aims to investigate the molecular epidemiology and clinical characteristics of EV-D68-associated SARI cases from South India. We screened influenza-negative archived throat swab specimens from Influenza-Like Illness (ILI) and SARI cases (n=959; 2016 to 2018 period) for enteroviruses by pan-enterovirus real-time RT-PCR. Thirteen samples positive for enteroviruses were typed by PCR and sequencing based on VPI, VP2 and/or 5′NCR regions. One EV-D68 RNA sample was subjected to next-generation sequencing for whole genome characterisation. Among 13 enterovirus cases, four were ECHO-11, three EV-D68, two CV-A16 and one each EV-71, CV-B1, CV-B2 and CV-A9. All three cases of EV-D68 infection were reported in children below 2 years of age from Kerala state of South India during June and July 2017. The patients developed pneumonia without any neurological complications. Sequencing based on VPI and 5′NCR regions showed that EV-D68 strains belong to the novel subclade B3. The EV-D68 complete genome identified with two unique amino acid substitutions in VP1 (T-246-I) and 3D (K-344-R) regions. This study reiterates the EV-D68 novel subclade B3 circulation in India and indicates the urgent need for structured EV-D68 surveillance in the country to describe the epidemiology.

中文翻译:

南印度儿童肠病毒D68与肺炎相关的遗传分析

EV-D68是与严重急性呼吸道疾病(SARI),急性弛缓性脊髓炎(AFM)和急性弛缓性麻痹(AFP)相关的新兴肠病毒感染。尽管全球报告了EV-D68暴发和零星病例,但印度却报告了一个病例。本研究旨在调查南印度与EV-D68相关的SARI病例的分子流行病学和临床特征。我们通过全肠病毒实时RT-PCR筛选了流感样疾病(ILI)和SARI病例(n = 959; 2016至2018年)的流感阴性归档咽拭子标本。通过PCR和基于VPI,VP2和/或5'NCR区的测序,对13株肠病毒呈阳性的样品进行了分型。对一个EV-D68 RNA样品进行了下一代测序,以进行全基因组表征。在13宗肠病毒病例中,其中4架是ECHO-11、3架EV-D68、2架CV-A16,每架EV-71,CV-B1,CV-B2和CV-A9。2017年6月至2017年7月期间,印度南部喀拉拉邦2岁以下儿童均报告了所有三例EV-D68感染。患者出现肺炎,无任何神经系统并发症。基于VPI和5'NCR区域的测序表明,EV-D68菌株属于新型子B3。EV-D68完整基因组在VP1(T-246-I)和3D(K-344-R)区域具有两个独特的氨基酸取代。这项研究重申了EV-D68新型子B3子气在印度的流行,并指出该国迫切需要进行结构化的EV-D68监测以描述流行病学。2017年6月至2017年7月期间,印度南部喀拉拉邦2岁以下儿童均报告了所有三例EV-D68感染。患者出现肺炎,无任何神经系统并发症。基于VPI和5'NCR区域的测序表明,EV-D68菌株属于新型子B3。EV-D68完整基因组在VP1(T-246-I)和3D(K-344-R)区域具有两个独特的氨基酸取代。这项研究重申了EV-D68新型子B3子气在印度的流行,并指出该国迫切需要进行结构化的EV-D68监测以描述流行病学。2017年6月至2017年7月期间,印度南部喀拉拉邦2岁以下儿童均报告了所有三例EV-D68感染。患者出现肺炎,无任何神经系统并发症。基于VPI和5'NCR区域的测序表明,EV-D68菌株属于新型子B3。EV-D68完整基因组在VP1(T-246-I)和3D(K-344-R)区域具有两个独特的氨基酸取代。这项研究重申了EV-D68新型子B3子气在印度的流行,并指出该国迫切需要进行结构化的EV-D68监测以描述流行病学。基于VPI和5'NCR区域的测序表明,EV-D68菌株属于新型子B3。EV-D68完整基因组在VP1(T-246-I)和3D(K-344-R)区域具有两个独特的氨基酸取代。这项研究重申了EV-D68新型子B3子气在印度的流行,并指出该国迫切需要进行结构化的EV-D68监测以描述流行病学。基于VPI和5'NCR区域的测序表明,EV-D68菌株属于新型子B3。EV-D68完整基因组在VP1(T-246-I)和3D(K-344-R)区域具有两个独特的氨基酸取代。这项研究重申了EV-D68新型子B3子气在印度的流行,并指出该国迫切需要进行结构化的EV-D68监测以描述流行病学。
更新日期:2021-05-18
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