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Genotyping of Non-Polio Enteroviruses Associated with Acute Flaccid

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Genotyping of Non-Polio Enteroviruses Associated with Acute Flaccid Onvimala et al. Virol J (2021) 18:153 https://doi.org/10.1186/s12985-021-01621-0 RESEARCH Open Access Genotyping of non-polio enteroviruses associated with acute faccid paralysis in Thailand in 2013 and 2014 Napa Onvimala1,2, Nathamon Kosoltanapiwat1, Pornpan Pumirat1, Muthita Vanaporn1, Suchitra Nimmanitya3, Ratana Tacharoenmuang2, Ratigorn Guntapong2 and Pornsawan Leaungwutiwong1* Abstract Background: Acute faccid paralysis (AFP) surveillance was conducted as part of the World Health Organization’s strategy for completely eradicating poliomyelitis and leaving non-polio enteroviruses NPEVs as one of the main potential causes of AFP. We aimed to detect NPEV in association with AFP. Methods: We used 459 isolates reported to be Negative Polio and some NPEVs by the World Health Organization Polio Regional Reference Laboratory (Thailand), which had been obtained during polio surveillance programmes conducted in Thailand in 2013–2014. Of 459 isolates, 35 belonged to the genus Enterovirus by RT-PCR and genotyp- ing by DNA sequencing. Results: This study found 17 NPEV genotypes, with 3, 13 and 1 belonging to enterovirus (EV) species A (EV-A), EV-B, and EV-C, respectively. The EV-A types identifed included coxsackievirus A2 (CA2), CA4, and EV71, typically associated with hand, foot and mouth diseases. EV-B is the most prevalent cause of AFP in Thailand, while CA21 was the only type of EV-C detected. The EV-B species (13/35; 76.5%) constituted the largest proportion of isolates, followed by EV-A (3/35; 17.6%) and EV-C (1/35; 5.9%). For the EV-B species, Echovirus (E) 30 and CVB were the most frequent isolates. E30, CVB, E14, and E6 were considered endemic strains. Conclusion: NPEVs, e.g. CA4, are reported for the frst time in Thailand. Despite some limitations to this study, this is the frst report on the circulation patterns of NPEVs associated with AFP in Thailand. AFP surveillance has unearthed many unknown NPEVs and, the cases of death due to AFP occur annually. Therefore, it is important to study NPEVs in the wake of the eradication of poliovirus in the context of the continued incidence of paralysis. Keywords: Acute faccid paralysis (AFP), Non-polio enteroviruses (NPEVs), Enterovirus (EV), Coxsackievirus (CA) Background cause of AFP can cause poliomyelitis. In March 2014, Acute faccid paralysis is a clinical syndrome, which refer Tailand completely eradicated poliomyelitis and left to a symptom of paralysis or weakness. Tere is much non-polio enteroviruses as one of the main potential cause of infectious and non-infectious. It can be cause causes of AFP [1]. So, we aimed to highlight the role of by many diseases such as poliomyelitis, enteritis, myosi- NPEV in association with AFP start from the year before tis, meningitis and encephalitis. Poliovirus was the main and after eradicate. Enterovirus is a genus belonging to the family Picornaviridae [2–4]. According to the classif- *Correspondence: [email protected] cation, 12 species can cause disease in both humans and 1 Department of Microbiology and Immunology, Faculty of Tropical animals [5–9]. However, 4 species of Enterovirus A-D Medicine, Mahidol University, Bangkok, Thailand and 3 species of Rhinovirus causes disease in humans. Full list of author information is available at the end of the article © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. The Creative Commons Public Domain Dedication waiver (http:// creat iveco mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Onvimala et al. Virol J (2021) 18:153 Page 2 of 8 Enterovirus E-L causes disease in animals. Enteroviruses Reference Laboratory (RRL) for polio screening at the A (EVA), B, C, and D, consist of 25, 63, 23, and 5 types National Institute of Health, Department of Medical Sci- respectively. Rhinoviruses A, B and C are composed of ence, Ministry of Public Health, Tailand (Fig. 1). Te 80, 32, and 57 types, while some are pending classifca- samples were isolated in RD and L20B for detected polio. tion [2, 3]. Currently studies on non-polio enterovirus Tis step was done by RRL of Tailand. All of them re- are being conducted in many countries, but the entero- inoculated in RD, Hep2 and Vero for increase the chance virus isolated varies in each country [10–17]. Te AFP to isolate more NPEV. surveillance system available in each country can detect non polio enteroviruses some are rare types such as RNA extraction and RT‑PCR typing EVC95 EVC105 in Northern India, EVC99 and EVA120 In this study, we confrmed the status of NPEV using in Nigeria [18, 19], so it is necessary to study the iso- reverse transcription polymerase chain reaction (RT- lated enterovirus genotype as a source for further study PCR). Total RNA was extracted from positive isolated of in each country. In Tailand, the last wild poliovirus stool samples stored at -20 degree Celsius using QIAamp was reported in 1997 [20], and Tailand was declared Viral RNA Extraction Kit (Cat. No. 52906; Qiagen). polio-free in 2014. Te detection of Enteroviruses in Among these unidentifed isolates, 24 NPEVs (5.2%) AFP patients plays an important role when an entero- were isolated in 2013 and 2014 and were confrmed to virus is found in an AFP surveillance cluster outbreak. be NPEVs by performing viral culture within 14 days at Over the years, the number of poliomyelitis cases has RRL; fnally, 11 NPEV isolates were re-inoculate in more reduced worldwide, and the disease has been eradicated cell culture RD, Vero, Hep2, GL-37 the positive was show in some parts of the world, leaving NPEV as one of the CPE within 14 days we observed CPE under micro- main potential causes of AFP. Regarding NPEVs identi- scope and used all positive for analysis in this study. 35 fed by AFP surveillance in Tailand in 2013 and 2014, positive isolates on analysis using pan-EV primers VP1 almost 50% were untyped, based on WHO protocols for region of the Enterovirus surveillance guidelines. Te EV detection [21]. Many researchers found NPEVs in typing was not performed on all RD-positive isolates as AFP patients [22–25]. EVA71 are a public health prob- per the timeframe set by the WHO, according to which lem in Tailand and can lead to death. A study of the role the result must be released within 14 days of receipt of of EVA71 in Brazil showed a resultant link to some AFP specimens. Tis study was not part of the routine surveil- cases [26]. Terefore, we must be alert for NPEV in AFP lance programme based on the typing of all NPEV iso- cases. Against this background, identifying the genotypes lates; therefore, we identifed EVs using universal pan-EV circulating in the country may improve our understand- primers with RT-PCR specifc to the viral polyprotein 1 ing of the epidemiology of EV infection; moreover, in the (VP1) region as universal primers of EV [27]. We used a wider context of polio eradication, it may provide assur- two-step RT-PCR. Te frst step for cDNA amplifcation ance that Poliovirus is not being overlooked. Laboratory by using four primers which were specifc to enterovirus data were analysed to provide an overview of the NPEV group A B C and D then performed the second step of genotypes identifed and their occurrence, diversity, and PCR for pan enterovirus VP1 region (Table 1). patterns of circulation in cases of AFP identifed in Tai- land in 2013 and 2014. VP1 sequencing Further, genotypes were analyzed by DNA sequenc- Methods ing. Te purifed PCR products were sent for chain-ter- Ethics approval mination DNA sequencing (Macrogen, Seoul, Korea). Te samples in this study were the unidentifed isolate Te nucleotide sequences were aligned with reference from AFP surveillance at the RRL, National Institute of sequences of EV genotypes obtained from the GenBank Health and discard non polio AFP by expert review com- database using ClustalW in BioEdit version 7.2.6.1. Te mittee from Department of Medical Science, Depart- phylogenetic tree was constructed with the maximum ment of Disease Control and Bureau of Epidemiology, likelihood and Bayesian methods with 1,000 bootstrap Ministry of Public Health, Nonthaburi, Tailand. So, we replicates using the MEGA 7 software. didn’t need an ethical approval to conduct the research. Results Virus isolated samples All 459 originally unidentifed isolates isolated from RD Tis study focused on a total of 459 isolates from patients cells and reported to be NPEVs were confrmed to be with AFP aged < 15 years who were identifed by AFP sur- EVs by RT-PCR specifc to the VP1 region. Viral RNA veillance in Tailand in 2013 and 2014. Te stool samples was extracted from the unidentifed isolates using four from 71 provinces were sent to the WHO Polio Regional primers specifc to EV groups A, B, C and D, as described Onvimala et al.
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