Direct identification of non-polio enteroviruses in residual paralysis cases by analysis of VP1 sequences

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.

Molecular characterization of non-polio enteroviruses isolated from children with acute flaccid paralysis in IRAN, 2015-2018

In addition to polioviruses, non-polio enteroviruses (NPEVs) are frequently isolated from patients with acute flaccid paralysis (AFP) worldwide. In polio-free countries, there have been expectations that with disappearing wild poliovirus from the community, the rate of AFP would decrease, but the increasing number of AFP cases proved this notion to be wrong. There are speculations that NPEVs might be the cause of increasing AFP rate. The aim of this study was to investigate frequency, genetic diversity, circulation patterns of NPEVs isolated from AFP cases in Iran from 2015 to 2018. Fifty-three NPEVs were isolated from stool specimens of AFP cases during four years of AFP surveillance. Nested PCR and VP1 sequencing revealed 20 NPEV types in which Echovirus 3 (13.2%), Echovirus 6 (13.2%), Echovirus 7 (7.5%), Echovirus 13 (7.5%) and Echovirus 21 (7.5%) were the most frequent. Coxsackie B viruses were isolated for the first time in AFP cases in Iran. The phylogenetic analysis of Echovirus 3 and Echovirus 6 revealed that Iranian echovirus strains belonged to the same cluster, indicating these viruses have been circulating in Iran for a long time. Compared to global Echovirus 3 and Echovirus 6 references, Echovirus 3 and Echovirus 6 strains detected in this study were closely related to Indian and Malaysia strains, respectively. The results of this study demonstrated a wide variety of NPEV types in Iranian patients, some of which had not been reported in previous studies. Moreover, this study highlights the need for NPEV surveillance in AFP cases.

Extending the utility of the WHO recommended assay for direct detection of enteroviruses from clinical specimen for resolving poliovirus co-infection

OBJECTIVES

In a polio-free world there might be reduced funding for poliovirus surveillance. There is therefore the need to ensure that enterovirologist globally, especially those outside the global polio laboratory network, can participate in poliovirus surveillance without neglecting their enterovirus type of interest. To accomplish this, assays are needed that allow such active participation.

RESULTS

In this study we describes a sensitive and specific utility extension of the recently recommended WHO RT-snPCR assay that enables independent detection of the three poliovirus types especially in cases of co-infection. More importantly, it piggy-backs on the first round PCR product of the WHO recommended assay and consequently ensures that enterovirologists interested in nonpolio enteroviruses can continue their investigations, and contribute significantly and specifically to poliovirus surveillance, by using the excess of their first round PCR product.

Preponderance of enterovirus C in RD-L20B-cell-culture-negative stool samples from children diagnosed with acute flaccid paralysis in Nigeria

Recently, a reverse transcriptase semi-nested polymerase chain reaction (RT-snPCR) assay was recommended by the WHO for direct detection of enteroviruses in clinical specimens. In this study, we use this assay and a modification thereof to screen acute flaccid paralysis (AFP) samples that had previously tested negative for enteroviruses by the RD-L20B algorithm. Thirty paired stool suspensions collected in 2015 as part of the national AFP surveillance program in different states of Nigeria were analyzed in this study. The samples had previously tested negative for enteroviruses in the polio laboratory in accordance with the WHO-recommended RD-L20B-cell-culture-based algorithm. Two samples that had previously been found to contain enteroviruses were included as positive controls. All samples were subjected to RNA extraction, the RT-snPCR assay and a modified version of the RT-snPCR. All amplicons were sequenced, and enteroviruses were identified using the enterovirus genotyping tool and phylogenetic analysis. Amplicons were recovered from the two controls and 50% (15/30) of the samples screened. Fourteen were successfully typed, of which, 7.1% (1/14), 21.4% (3/14), 64.3% (9/14) and 7.1% (1/14) were enterovirus (EV) -A, EV-B, EV-C and a mixture of EV-B and C (EV-C99 and E25), respectively. The two controls were identified as EV-C99 and coxsackievirus (CV) -A1, both of which belong to the species Enterovirus C. In one sample, poliovirus serotype 2 was detected and found to have the VP1 _ILE143 variation and was therefore identified as a vaccine strain. The results of this study showed that significant proportion of enterovirus infections (including some with Sabin PV2) are being missed by the RD-L20B-cell-culture-based algorithm, thus highlighting the value of the RT-snPCR assay and its modifications. The circulation and preponderance of EV-C in Nigeria was also confirmed.

Non-polio Enteroviruses in Karnataka, India: Virological surveillance of acute flaccid paralysis cases (July 1997-2013)

BACKGROUND AND OBJECTIVES

Since 1997 National Institute of Virology, Bangalore Unit involved in WHO's Acute flaccid paralysis paediatric cases surveillance programme to isolate and detect polioviruses. Stool samples yielded not only polioviruses but also Non-Polio enteroviruses. This report is an overview of non-polio Enterovirus (NPEV) epidemiology in Karnataka state, India for the period of 16-years and 6 months from July 1997-2013.

METHODS

A total of 19,410 clinical samples were processed for virus isolation as a part of acute flaccid paralysis (AFP) surveillance for Global Polio Eradication Programme in India at National Polio Laboratory, at Bengaluru. NPEV detection was performed by virus isolation on cell culture according to World Health Organisation recommended protocols.

RESULTS

A total of 4152 NPEV isolates were obtained. The NPEV isolation rate varied from year to year but with a total NPEV rate of 21.39%.

CONCLUSION

A seasonal variation was noted with high transmission period between April and October with peaks in June-July. The male to female ratio was 1:1.2. The isolation of NPEV decreased significantly with the increase in age. Epidemiology of NPEVs from AFP cases in Karnataka is described.

Echovirus serotypes circulating in Malaysia from 2002 to 2013

OBJECTIVE

To identify the circulating serotypes of human echovirus in Malaysia from 2002 to 2013.

METHODS

A total of 31 retrospective samples from non-polio acute flacid paralysis, hand-food-and-mouth disease, viral meningitis and enterovirus cases were subjected to amplification of partial VP1 gene by RT-PCR.

RESULTS

Sequencing and phylogenetic analysis of the partial sequences identified presence of human echovirus and human coxsackie viruses. It was found that echovirus 11 was the commonly circulating serotype followed by echovirus 6, echovirus 7, echovirus 3, echovirus 9, echovirus 30 and echovirus 1 in decreasing order. Additionally two types of human coxsackie virus isolates were detected which were coxsackie A24 and B3.

CONCLUSIONS

From the findings, there is a possibility that echovirus 11 is the predominant serotype among Malaysian patients with echovirus infection. However, a larger sample size will yield a more confident result to support this evidence.

Bioinformatics analysis and genetic diversity of the poliovirus

Poliomyelitis, a disease which can manifest as muscle paralysis, is caused by the poliovirus, which is a human enterovirus and member of the family Picornaviridae that usually transmits by the faecal-oral route. The viruses of the OPV (oral poliovirus attenuated-live vaccine) strains can mutate in the human intestine during replication and some of these mutations can lead to the recovery of serious neurovirulence. Informatics research of the poliovirus genome can be used to explain further the characteristics of this virus. In this study, sequences from 100 poliovirus isolates were acquired from GenBank. To determine the evolutionary relationship between the strains, we compared and analysed the sequences of the complete poliovirus genome and the VP1 region. The reconstructed phylogenetic trees for the complete sequences and the VP1 sequences were both divided into two branches, indicating that the genetic relationships of the whole poliovirus genome and the VP1 sequences are very similar. This branching indicates that the virulence and pathogenicity of poliomyelitis may be associated with the VP1 region. Sequence alignment of the VP1 region revealed numerous mutation sites in which mutation rates of >30 % were detected. In a group of strains recorded in the USA, mutation sites and mutation types were the same and this may be associated with their distribution in the evolutionary tree and their genetic relationship. In conclusion, the genetic evolutionary relationships of poliovirus isolate sequences are determined to a great extent by the VP1 protein, and poliovirus strains located on the same branch of the phylogenetic tree contain the same mutation spots and mutation types. Hence, the genetic characteristics of the VP1 region in the poliovirus genome should be analysed to identify the transmission route of poliovirus and provide the basis of viral immunity development.

Genotyping of human parechoviruses in Iranian young children with aseptic meningitis and sepsis-like illness

Human parechoviruses (HPeV) are classified into 14 genotypes. HPeV1 and HPeV2 are the most prevalent genotypes in young children, which have been associated with mild to severe diseases. This study was conducted to investigate the involvement of HPeVs in aseptic meningitis and sepsis-like illness in Iran. Viral RNA was extracted from 148 cerebrospinal fluid samples from children <8 years old with primary diagnosis of aseptic meningitis and/or sepsis-like illness. Specific HPeV, HEV real-time PCR and HPeV typing were done to identify the infection rate of these viruses. HPeV and HEV were detected in 64 (43.24 %), 31 (20.94 %) of 148 patients with 10 (6.75 %) coinfection. VP1/VP3 junction region was successfully sequenced from 12 of the HPeV-positive specimens, and all of them were identified as HPeV1. HPeV was more prevalent than HEV in both aseptic meningitis and sepsis-like illness, so further studies are needed to understand the disease burden of HPeV infections, and clinical manifestations especially in specific illnesses of possible viral etiology. Direct detection of these viruses leads to reduce hospitalization and use of antibiotic, which are often followed by other complications in neonates and young children.

An automated genotyping tool for enteroviruses and noroviruses

BACKGROUND

Molecular techniques are established as routine in virological laboratories and virus typing through (partial) sequence analysis is increasingly common. Quality assurance for the use of typing data requires harmonization of genotype nomenclature, and agreement on target genes, depending on the level of resolution required, and robustness of methods.

OBJECTIVE

To develop and validate web-based open-access typing-tools for enteroviruses and noroviruses.

STUDY DESIGN

An automated web-based typing algorithm was developed, starting with BLAST analysis of the query sequence against a reference set of sequences from viruses in the family Picornaviridae or Caliciviridae. The second step is phylogenetic analysis of the query sequence and a sub-set of the reference sequences, to assign the enterovirus type or norovirus genotype and/or variant, with profile alignment, construction of phylogenetic trees and bootstrap validation. Typing is performed on VP1 sequences of Human enterovirus A to D, and ORF1 and ORF2 sequences of genogroup I and II noroviruses. For validation, we used the tools to automatically type sequences in the RIVM and CDC enterovirus databases and the FBVE norovirus database.

RESULTS

Using the typing-tools, 785(99%) of 795 Enterovirus VP1 sequences, and 8154(98.5%) of 8342 norovirus sequences were typed in accordance with previously used methods. Subtyping into variants was achieved for 4439(78.4%) of 5838 NoV GII.4 sequences.

DISCUSSION AND CONCLUSIONS

The online typing-tools reliably assign genotypes for enteroviruses and noroviruses. The use of phylogenetic methods makes these tools robust to ongoing evolution. This should facilitate standardized genotyping and nomenclature in clinical and public health laboratories, thus supporting inter-laboratory comparisons.