Detection of enteroviruses by reverse-transcriptase polymerase chain reaction in cell culture negative stool specimens of patients with acute flaccid paralysis

Molecular typing of enteroviruses and parechoviruses in acute flaccid paralysis patients in Iran in 2019

Enteroviruses (EVs) and parechoviruses (PeVs) are among the viral pathogens that can cause acute flaccid paralysis (AFP). There is not sufficient information about direct detection of EVs and PeVs in AFP patients in Iran. The aim of this study was to conduct a one-year study for direct detection and molecular typing of EVs and PeVs from stool samples of AFP patients in Iran. One hundred stool samples from polio-negative AFP patients who were referred to the Iran National Polio Laboratory were randomly chosen and analyzed during 2019. A one-step TaqMan probe-based real-time RT-PCR assay targeting the 5'-untranslated region (5' -UTR) was used to screen for EVs and PeVs. All positive samples were genotyped by direct sequencing, targeting the VP1 region of the genome. In total, twelve (12%) and four (4%) stool samples from polio-negative AFP children were positive for EVs and PeVs, respectively. Sequence analysis revealed the presence of echovirus 2 (E2), echovirus 13 (E13), echovirus 25 (E25), echovirus 30 (E30), coxsackievirus A2 (CVA2), coxsackievirus A9 (CVA9), coxsackievirus A16 (CVA16), human enterovirus A76 (HEV-A76), and human parechovirus 1 (HPeV1) in children with AFP-like symptoms. Phylogenetic analysis showed that E2 strains clustered together with the strains circulating in the Netherlands during 2014, whereas the PeV strains belonged to different lineages. This study demonstrates that different EV types are associated with AFP cases in Iran. However, the frequency of association of PeVs with AFP cases appears to be low.

Assessment of enteroviruses from sewage water and clinical samples during eradication phase of polio in North India

Background

The Enterovirus (EV) surveillance system is inadequate in densely populated cities in India. EV can be shed in feces for several weeks; these viruses are not easily inactivated and may persist in sewage for long periods. Surveillance and epidemiological study of EV-related disease is necessary.

Methods

In this study, we compare the EV found in sewage with clinically isolated samples. Tissue culture was used for isolation of the virus and serotype confirmed by enterovirus neutralization tests.

Results

We found positive cases for enterovirus from clinical and sewage samples and identified additional isolates as echovirus 9, 11, 25 & 30 by sequencing.

Conclusion

There is a close relation among the serotypes of enterovirus shed in stools and isolated from the environment but few serotypes which were detected in sewage samples were not found clinically and the few which were detected clinically not found in sewage because some viruses are difficult to detect by the cell culture method.This study will be helpful for the researchers who are working on polio and nonpolio enterovirus especially in the countries which are struggling for polio eradication.

Association analysis of polymorphisms in OAS1 with susceptibility and severity of hand, foot and mouth disease

Hand, foot and mouth disease (HFMD) is a common childhood illness that mainly affects Asian children under the age of 5 years. Human enterovirus 71 (EV71) and coxsackievirus A16 (CA16) are the most common pathogens of HFMD. It is imperative that the susceptible population is screened early and that the severe illness population can be identified via genetic variation detection in children. Four single-nucleotide polymorphisms (SNP) [2'-5'-oligoadenylate synthetase1 (OAS1) rs10774671, selectin P ligand (SELPLG) rs2228315, scavenger receptor class B member 2 (SCARB2) rs41284767 and interleukin 28B (IL28B) rs12979860] were determined by Taqman assays in 333 HFMD samples and 163 control samples. The rs2228315, rs41284767 and rs12979860 polymorphisms did not differ significantly between HFMD patients and the controls, but the prevalence of the rs10774671 polymorphism was significantly different between the control children and children infected with CA16 (GG genotype vs. AA + AG genotype, P < 0.05). Children with the GG genotype were more susceptible to CA16-type HFMD. Furthermore, the rs10774671 genotype distribution was clearly different between children with severe HFMD and those with mild HFMD [P < 0.05, OR 0.240, 95% CI (0.071-0.809)]. HFMD children with the AA+AG genotype were more likely to progress to encephalitis than were those with the GG genotype. Plasma γ-interferon (IFN) expression levels among control children and the mild and severe HFMD children were detected by ELISA. Those with mild HFMD had higher γ-IFN expression levels compared with those with severe HFMD (P < 0.05). In addition, there is a significant correlation between γ-IFN levels and OAS1 rs10774671 SNP, as analysed by linear correlation assay. The GG genotype correlated with higher γ-IFN levels (P < 0.05). In short, the OAS1 rs10774671 SNP GG genotype contributed to CA16 susceptibility and was associated with the development of mild HFMD.

Human parechovirus genotypes -10, -13 and -15 in Pakistani children with acute dehydrating gastroenteritis

Human parechoviruses are known to cause asymptomatic to severe clinical illness predominantly respiratory and gastroenetric infections. Despite their global prevalence, epidemiological studies have not been performed in Pakistan. In this study, we retrospectively analyzed 110 fecal specimen and found 26 (24%) positive for viral RNA with HPeV-10 (n = 3, 23%), HPeV-13 (n = 4, 31%) and HPeV-15 (n = 6, 46%) genotypes. Clinical features of patients with different HPeV genotypes were compared. All HPeV positive children were aged ≤4 years (mean 13.92 months). The male-to-female ratio was 1: 1.17 (46.2 vs 53.8%) with significant association (p = .031) to HPeV infectivity. HPeV-10 and -13 were found during summer while HPeV-15 was only detected during late winter season. Disease symptoms were more severe in children infected with HPeV-10 and -13 as compared to HPeV-15. Fever and vomiting were observed in 100% cases of HPeV-10 and -13 while only 17% patients of HPeV-15 had these complaints. Phylogenetic analyses showed that HPeV-10, -13 and -15 strains found in this study have 9-13%, 16.8% and 21.8% nucleotide divergence respectively from the prototype strains and were clustered to distinct genetic lineages. This is the first report of HPeV-15 infection in humans although first identified in rhesus macaques. The arginine-glycine-aspartic acid (RGD) motif present at the C-terminal of VP1 responsible for the viral attachment to cellular integrins was not found in all of these strains. In conclusion, these findings enhance our knowledge related to the epidemiology and genetic diversity of the HPeV in Pakistan and support the need for continued laboratory based surveillance programs especially in infants and neonatal clinical settings. Further, the parechovirus pathogenesis, cross-species transmission and disease reservoirs must be ascertained to adopt better prevention measures.

Diversity of picornaviruses in rural Bolivia

The family Picornaviridae is a large and diverse group of viruses that infect humans and animals. Picornaviruses are among the most common infections of humans and cause a wide spectrum of acute human disease. This study began as an investigation of acute flaccid paralysis (AFP) in a small area of eastern Bolivia, where surveillance had identified a persistently high AFP rate in children. Stools were collected and diagnostic studies ruled out poliovirus. We tested stool specimens from 51 AFP cases and 34 healthy household or community contacts collected during 2002-2003 using real-time and semi-nested reverse transcription polymerase chain reaction assays for enterovirus, parechovirus, cardiovirus, kobuvirus, salivirus and cosavirus. Anecdotal reports suggested a temporal association with neurological disease in domestic pigs, so six porcine stools were also collected and tested with the same set of assays, with the addition of an assay for porcine teschovirus. A total of 126 picornaviruses were detected in 73 of 85 human individuals, consisting of 53 different picornavirus types encompassing five genera (all except Kobuvirus). All six porcine stools contained porcine and/or human picornaviruses. No single virus, or combination of viruses, specifically correlated with AFP; however, the study revealed a surprising complexity of enteric picornaviruses in a single community.

Enteroviral central nervous system infections in children of the region of monastir, Tunisia: diagnosis, laboratory findings of cerebrospinal fluid and clinical manifestations

Human enteroviruses (HEV) are one of the major causes of central nervous system (CNS) infections in pediatrics. A prospective study was conducted to assess the epidemiological, clinical, and laboratory characteristics of enterovirus (EV) infections of the CNS in children under 15-years-old, suspected of having viral CNS infections and admitted to the Pediatric Department of Monastir University Hospital, Tunisia. Enteroviral RNA was detected by 5' NCR nested RT-PCR assay in 33 % (20 out of 60) of cerebrospinal fluid specimens, whereas only six samples (10 %) were EV positive in cell culture. EV-positive patients were clustered according to their clinical manifestations, predominantly diagnosed as aseptic meningitis (65 %) and meningoencephalitis (20 %). Fever, headache, vomiting, and neck stiffness were the most pronounced symptoms. Pleocytosis with the predominance of lymphocytes was observed in 60 % of EV positive specimens. Although patients suffering from EV infections were encountered throughout the year, most occurred during spring and summer months. Using VP1-2A nested RT-PCR and sequence analysis, three of the 20 positive HEV were identified as Echovirus (E)-9. This is the first report of a cluster of aseptic meningitis cases caused by E-9 in Monastir.

Enterovirus and herpesviridae family as etiologic agents of lymphomonocytary meningitis, Southern Brazil

Viral meningitis is a common infectious disease of the central nervous system (CNS) that occurs worldwide. The aim of this study was to identify the etiologic agent of lymphomonocytary meningitis in Curitiba, PR, Brazil. During the period of July 2005 to December 2006, 460 cerebrospinal fluid (CSF) samples with lymphomonocytary meningitis were analyzed by PCR methodologies. Fifty nine (12.8%) samples were positive. Enteroviruses was present in 49 (83%) samples and herpes virus family in 10 (17%), of these 6 (10%) herpes simplex virus, 1 (2%) Epstein Barr virus, 2 (3%) human herpes virus type 6 and 1 (2%) mixed infection of enterovirus and Epstein Barr virus. As conclusion enterovirus was the most frequent virus, with circulation during summer and was observed with higher frequency between 4 to 17 years of age. PCR methodology is an important method for rapid detection of RNA enterovirus and DNA herpesvirus in CSF.

Non-polio enteroviruses in acute flaccid paralysis children of India: vital assessment before polio eradication

AIM

This study is an overview of non-polio enterovirus (NPEV) circulating in North India studied from the perspective of poliomyelitis eradication. Wild polio cases declined because of intensive oral polio vaccine immunization. As we approach global eradication of poliovirus (PV), NPEV causing acute flaccid paralysis (AFP) are equal cause of concern.

METHODS

A total of 46 653 AFP samples (World Health Organization) and apparently 1000 healthy contacts living in the same geographical area were studied (2004-2007). Serological identification of NPEV was done using RIVM-specific pools (The Netherlands). Untyped (UT)-NPEVs were sequenced directly from reverse transcription-polymerase chain reaction using pan-enterovirus (Pan-EV) primer (CDC, Atlanta, GA) targeting highly conserved 5'un-translated regions of the enterovirus.

RESULTS

In this study, 12 513 NPEVs were isolated from the collected stool samples. Seroneutralization had identified 67% of NPEV isolates, whereas 32.6% remained as UT- NPEV. Of the typed NPEVs, Coxsackie-B accounted for 32.3%; followed by echoviruses-11, 12, 13, 7 between 8 and 28%. In sequencing few UT-NPEVs, some were identified also as echovirus-30, 11 and 18 which were probably present in mixtures as they remained UT-NPEV in ENT. Newly classified human enterovirus virus-86 (HEV) (EU079026), HEV-97(EU071767) and HEV-B isolate (EU071768) were isolated in AFP samples.

CONCLUSIONS

This study provided definitive information about circulation, prevalence and new emerging NPEV in the polio-endemic region of India, hence they should be considered in AFP surveillance. This would help in adopting and planning new strategies in post-PV eradication era in the country. This is the right time to prepare for the future tasks while we head towards a polio-free region.