Genotyping of enteroviruses isolated in Kenya from pediatric patients using partial VP1 region

Diversity of enteroviruses in cerebrospinal fluid specimens collected from hospitalised patients in the private and public sector in South Africa

Enteroviruses cause a wide range of neurological illnesses such as encephalitis, meningitis, and acute flaccid paralysis. Two types of enteroviruses, echovirus E4 and E9, have recently been detected in South Africa and are known to be associated with meningitis and encephalitis. The objective of this study was to characterize enterovirus strains detected in cerebrospinal fluid specimens of hospitalized patients in the private and public sector to identify genotypes associated with meningitis and encephalitis. From January 2019 to June 2021 enterovirus positive nucleic acid samples were obtained from a private (n = 116) and a public sector (n = 101) laboratory. These enteroviruses were typed using a nested set of primers targeting the VP1 region of the enterovirus genome, followed by Sanger sequencing and BLASTn analysis. Forty-two percent (91/217) of the strains could be genotyped. Enterovirus B species was the major species detected in 95% (86/91) of the specimens, followed by species C in 3% (3/91) and species A in 2% (2/91) of the specimens. Echovirus E4 and E9 were the two major types identified in this study and were detected in 70% (64/91) and in 10% (9/91) of specimens, respectively. Echovirus E11 has previously been identified in sewage samples from South Africa, but this study is the first to report Echovirus E11 in cerebrospinal fluid specimens from South African patients. The genotypes identified during this study are known to be associated with encephalitis and meningitis. The predominant detection of echovirus E4 followed by E9 corresponds with other studies conducted in South Africa.

Molecular Amplification and Cell Culturing Efficiency for Enteroviruses' Detection in Cerebrospinal Fluids of Algerian Patients Suffering from Meningitis

Enteroviruses (EVs) represent a major cause of viral meningitis, being responsible for nearly 1 billion infections each year worldwide. Several techniques were developed to obtain better diagnostic results of EV infections. Herein, we evaluated the efficiency of EV detection through isolation on both Rhabdomyosarcoma (RD) and Vero cell line cultures, conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR. Thus, 50 cerebrospinal fluid (CSF) samples belonging to patients suspected to have viral meningitis in northern Algeria were collected, anonymously numbered from 1 to 50 and subjected to the above-mentioned techniques for EV detection. Using real-time RT-PCR, 34 CSF samples were revealed to be positive for viral origin of meningitis (68%). Thirteen of them were positive when the conventional RT-PCR was used (26%), and only three samples gave positive results when the cell culture technique was used (6%). Surprisingly, two cell culture-positive CSF samples, namely, 31 and 39, were negative using RT-PCR directly on the original samples. However, they turned to be positive when amplification was carried out on their corresponding cell culture supernatant. The cell-cultured viral isolates were then identified by sequencing their viral genome's VP1 regions. All of them were revealed to belong to the echovirus 27 strain. This investigation demonstrates that RT-PCR techniques are often more sensitive, accurate and much faster, providing reliable results within a clinically acceptable timeframe. However, viral isolation on cell cultures remains crucial to obtain enough viral load for serological tests or even to avoid the rare, but existing, false negative PCR.

Analysing the interplay of environmental virology, public health, and sanitation: a comprehensive review from a Kenyan perspective

This comprehensive review examines the interplay between environmental virology, public health, and sanitation in the unique context of Kenya. The review sheds light on the specific viral threats faced by the country, including waterborne viruses, zoonotic infections, and emerging viral diseases, and their implications for public health. It explores the prevailing public health challenges in Kenya associated with environmental viromics, such as infectious viral diseases, and the rising burden of other infectious particles. The role of sanitation in mitigating viral infections is highlighted, emphasising the importance of clean water supply, proper waste management, and hygienic practises. The review also presents strategies for strengthening environmental virology research in Kenya, including enhancing laboratory capacities and leveraging technological advancements. Furthermore, the policy implications and recommendations derived from the review emphasise the need for multi-sectoral collaboration, evidence-based decision-making, and long-term investments in infrastructure and behaviour change interventions. Implementing these strategies can enhance the understanding of environmental virology, improve public health outcomes, and ensure sustainable sanitation practises in Kenya, ultimately contributing to the well-being of the population and sustainable development.

Molecular Detection of Enteric Viruses in Under-Five Children with Diarrhea in Debre Tabor, Northwest Ethiopia

Background

Viral gastroenteritis belongs to the major public health problems of infant and children worldwide. The largest proportion of morbidity and mortality occurs in Sub-Saharan Africa.

Purpose

Aimed to assess the burden and genetic diversity of enteric viruses among children with diarrhea.

Patients and Methods

A cross-sectional study was undertaken from December 2015 to April 2016 in Debre Tabor. A total of thirty-eight children, who presented with diarrhea at Debre Tabor health centers, were included. Fecal samples were collected and screened for enteric viruses by RT-PCR. Data were analyzed using SPSS software. Descriptive summary techniques were used to display the findings.

Results

Out of thirty-eight children screened, 52.6% were positive for at least one enteric virus. Six (30.0%) of the children had mixed enteric virus infections. Human adenovirus (HAdV) 7 (18.4%) was predominant followed by noroviruses (NoVs) 5 (13.2%), enterovirus (EV) 5 (13.2%), rotavirus A (RVA) 4 (10.5%), human astrovirus (HAstV) 2 (5.3%), and human parechovirus (HPeV) 1 (2.6%). Overall, nineteen different types of enteric virus genotypes were identified. Diverse adenovirus within species A (HAdV-12,-31), B (HAdV-3), C (HAdV-2), and F (HAdV-4) were detected. Norovirus II (GII.4 and GII.6) and norovirus I (GI.2, GI.3, and GI.5) genotypes were found. Sapovirus genotypes within genogroup II (GII.1, GII.5, and GII.6) were identified. Wild-type rotavirus G9 and P[8] genotypes were detected in one of the rotavirus positive samples. Non-polio enteroviruses within species A (coxsackie A virus (CAV) 5, CAV6, and CAV14) and C (enterovirus (EV-C) 99) were also identified. In two of the fecal samples classic HAstV-2 was detected.

Conclusion

Diverse enteric viruses were detected in fecal samples from under-five children with diarrhea. The detection of heterogeneous enteric viruses in this small data set highlights the need for extended multicenter studies to describe the burden and genetic diversity of enteric virus.

Molecular epidemiology of Enteroviruses and Rhinoviruses in patients with acute respiratory infections in Yaounde, Cameroon

Background

Acute respiratory infections (ARI) are associated with a huge morbidity and mortality worldwide. Rhinoviruses (RVs) and Enteroviruses (EVs) are recognized as leading causes of ARI.

Objectives

The present study describes the molecular epidemiology of RVs and EVs in Cameroon over a 3‐year surveillance period.

Methods

From September 2011 to October 2014, nasopharyngeal swabs were collected from patients with influenza‐like illness (ILI) and severe acute respiratory infections (SARI). Two sub‐genomic regions of the EVs and RVs were targeted for molecular characterization. These included the most conserved 5′‐untranslated region (5′UTR) and the viral protein 4/viral protein 2 transition region (VP4/VP2).

Results

A total of 974 samples were collected. Children ≤5 years accounted for 85.7% (835/974) of all participants. Among them, 160 (16.4%) were positive for RVs and/or EVs. RVs and/or EVs were significantly more identified in ILI compared to SARI patients (P = .015). Both viruses co‐circulated all year long with a marked increase of occurrence during rainy and cold season. All RV species were found to circulate in Cameroon, with 6, 10 and 6 virus types belonging to the RV‐A, RV‐B and RV‐C, respectively. EV species identified comprised EV‐A (1 Coxsackie virus A5), EV‐B (1 Coxsackie virus A9 and 2 Coxsackie virus B1) and EV‐C (1 EV‐C117).

Conclusions

This study indicates a strong year‐round occurrence of EV and RV associated respiratory infections in Cameroon. Molecular characterization identified a wide variety of RVs and EVs in patients with ARI in Cameroon.

Circulation and Molecular Epidemiology of Enteroviruses in Paralyzed, Immunodeficient and Healthy Individuals in Tunisia, a Country with a Polio-Free Status for Decades

This report is an overview of enterovirus (EV) detection in Tunisian polio-suspected paralytic cases (acute flaccid paralysis (AFP) cases), healthy contacts and patients with primary immunodeficiencies (PID) during an 11-year period. A total of 2735 clinical samples were analyzed for EV isolation and type identification, according to the recommended protocols of the World Health Organization. Three poliovirus (PV) serotypes and 28 different nonpolio enteroviruses (NPEVs) were detected. The NPEV detection rate was 4.3%, 2.8% and 12.4% in AFP cases, healthy contacts and PID patients, respectively. The predominant species was EV-B, and the circulation of viruses from species EV-A was noted since 2011. All PVs detected were of Sabin origin. The PV detection rate was higher in PID patients compared to AFP cases and contacts (6.8%, 1.5% and 1.3% respectively). PV2 was not detected since 2015. Using nucleotide sequencing of the entire VP1 region, 61 strains were characterized as Sabin-like. Among them, six strains of types 1 and 3 PV were identified as pre-vaccine-derived polioviruses (VDPVs). Five type 2 PV, four strains belonging to type 1 PV and two strains belonging to type 3 PV, were classified as iVDPVs. The data presented provide a comprehensive picture of EVs circulating in Tunisia over an 11-year period, reveal changes in their epidemiology as compared to previous studies and highlight the need to set up a warning system to avoid unnoticed PVs.

Molecular Epidemiological, Serological, and Pathogenic Analysis of EV-B75 Associated With Acute Flaccid Paralysis Cases in Tibet, China

Enterovirus B75 (EV-B75) is a newly identified serotype of the enterovirus B species. To date, only 112 cases related to EV-B75 have been reported worldwide, and research on EV-B75 is still limited with only two full-length genome sequences available in GenBank. The present study reported seven EV-B75 sequences from a child with acute flaccid paralysis and six asymptomatic close contacts in Shigatse, Tibet. Phylogenetic analysis revealed that the Tibetan strain was possibly imported from neighboring India. Seroepidemiological analyses indicated that EV-B75 has not yet caused a large-scale epidemic in Tibet. Similarity plots and boot scanning analyses revealed frequent intertypic recombination in the non-structural region of all seven Tibet EV-B75 strains. All seven Tibetan strains were temperature-sensitive, suggesting their poor transmissibility in the environment. Overall, though the seven Tibetan strains did not cause large-scale infection, prevention and control of the novel enterovirus cannot be underestimated.

Genotyping of enteroviruses and human parechoviruses highlights their diversity in Northwest Ethiopia

Enteroviruses (EVs) and human parechoviruses (HPeVs) infections are associated with various forms of disease, including gastroenteritis. As information on the molecular epidemiology of these viruses is limited in Ethiopia, the genetic diversity of EV and HPeV was investigated in the Northwestern part of the country. Of the total 450 stool samples obtained from infants and young children with diarrhea, 157 (34.9%) were positive for EV and 49 (10.9%) for HPeV RNA when tested by real-time reverse transcription polymerase chain reaction. Genotyping was performed by sequencing of the EV VP1 gene and the HPeV VP3/VP1 gene, respectively. Genotyping of EV was successful in 118 samples. Thereof, 82 (69.5%) belonged to non-polio EVs as a broad range of genotypes within species C, B, and A. Sabin polioviruses were found in 36 cases. HPeV sequences were also heterogeneous with a relative dominance of genotype 3. In conclusion, diverse EV and HPeV genotypes were found cocirculating in Northwest Ethiopia. The findings highlight the importance of continuous surveillance of these viruses in Ethiopia.

Cell culture demonstrates superior sensitivity over one step real time RT PCR and nested VP1 amplification for Enteroviruses

This study evaluated and compared the sensitivity profile of routine cell culture, nested VP1 amplification and one step real time RT PCR for Enteroviruses. Serially diluted spiked samples of four model viruses (EV71, CVA16, CVB5 and PV1) and 32 true positive samples including Poliovirus (PV1 & PV3), Coxsackie virus (CVB5, CVB3, CVB1 & CVA4, 10, 16), Echovirus (Echo 6, 7, 11, 13, 18, 25 & 30) and Enterovirus 71 (E71), and 32 true negative stool samples were subjected to cell culture, nested RT PCR and one step real time RT PCR. The result of sensitivity test indicated superior sensitivity with one step real time RT PCR (75 %, 24/32) against cell culture (71.9 %, 23/32) and nested RT PCR (65.6 %, 21/32). The most specific test was cell culture (100 %, 32/32), followed by nested RT PCR (96.9 %, 31/32). Positive predictive values were 100 %: 23/23, 95.5 %; 21/22 and 88.9 %; 24/27, for cell culture, nested RT PCR and one step real time RT PCR, respectively, and one step real time RT PCR had the highest negative predictive value (78.4 %, 29/37). Overall result indicate relatively high analytical sensitivity with all the tests, suggesting superior performance by cell culture. Therefore, cell culture is the gold standard. However, considering intensive nature of cell cultures and prolong window for results, it is wise to consider one step real time RT PCR in routine diagnosis for its added advantages. Meanwhile, selecting a combination of tests can maximize detection, depending on the laboratory strength.

Genetic Diversity Analysis of Coxsackievirus A8 Circulating in China and Worldwide Reveals a Highly Divergent Genotype

Coxsackievirus A8 (CV-A8) is one of the pathogens associated with hand, foot and mouth disease (HFMD) and herpangina (HA), occasionally leading to severe neurological disorders such as acute flaccid paralysis (AFP). Only one study aimed at CV-A8 has been published to date, and only 12 whole-genome sequences are publicly available. In this study, complete genome sequences from 11 CV-A8 strains isolated from HFMD patients in extensive regions from China between 2013 and 2018 were determined, and all sequences from GenBank were retrieved. A phylogenetic analysis based on a total of 34 complete VP1 sequences of CV-A8 revealed five genotypes: A, B, C, D and E. The newly emerging genotype E presented a highly phylogenetic divergence compared with the other genotypes and was composed of the majority of the strains sequenced in this study. Markov chain Monte Carlo (MCMC) analysis revealed that genotype E has been evolving for nearly a century and somehow arose in approximately 2010. The Bayesian skyline plot showed that the population size of CV-A8 has experienced three dynamic fluctuations since 2001. Amino acid residues of VP1100N, 103Y, 240T and 241V, which were embedded in the potential capsid loops of genotype E, might enhance genotype E adaption to the human hosts. The CV-A8 whole genomes displayed significant intra-genotypic genetic diversity in the non-capsid region, and a total of six recombinant lineages were detected. The Chinese viruses from genotype E might have emerged recently from recombining with European CV-A6 strains. CV-A8 is a less important HFMD pathogen, and the capsid gene diversity and non-capsid recombination variety observed in CV-A8 strains indicated that the constant generation of deleterious genomes and a constant selection pressure against these deleterious mutations is still ongoing within CV-A8 quasispecies. It is possible that CV-A8 could become an important pathogen in the HFMD spectrum in the future. Further surveillance of CV-A8 is greatly needed.

Assessing antigenic drift and phylogeny of influenza A (H1N1) pdm09 virus in Kenya using HA1 sub-unit of the hemagglutinin gene

Influenza A (H1N1) pdm09 virus emerged in North America in 2009 and has been established as a seasonal strain in humans. After an antigenic stasis of about six years, new antigenically distinct variants of the virus emerged globally in 2016 necessitating a change in the vaccine formulation for the first time in 2017. Herein, we analyzed thirty-eight HA sequences of influenza A (H1N1) pdm09 strains isolated in Kenya during 2015-2018 seasons, to evaluate their antigenic and molecular properties based on the HA1 sub-unit. Our analyses revealed that the A (H1N1) pdm09 strains that circulated in Kenya during this period belonged to genetic clade 6B, subclade 6B.1 and 6B.2. The Kenyan 2015 and 2016 isolates differed from the vaccine strain A/California/07/2009 at nine and fourteen antigenic sites in the HA1 respectively. Further, those isolated in 2017 and 2018 correspondingly varied from A/Michigan/45/2015 vaccine strain at three and fifteen antigenic sites. The predicted vaccine efficacy of A/California/07/2009 against Kenyan 2015/2016 was estimated to be 32.4% while A/Michigan/45/2015 showed estimated vaccine efficacies of 39.6% - 41.8% and 32.4% - 42.1% against Kenyan 2017 and 2018 strains, respectively. Hemagglutination-inhibition (HAI) assay using ferret post-infection reference antiserum showed that the titers for the Kenyan 2015/2016 isolates were 2-8-fold lower compared to the vaccine strain. Overall, our results suggest the A (H1N1) pdm09 viruses that circulated in Kenya during 2015/2016 influenza seasons were antigenic variants of the recommended vaccine strains, denoting sub-optimal vaccine efficacy. Additionally, data generated point to a swiftly evolving influenza A (H1N1) pdm09 virus in recent post pandemic era, underscoring the need for sustained surveillance coupled with molecular and antigenic analyses, to inform appropriate and timely influenza vaccine update.

Enterovirus D68 Subclade B3 Circulation in Senegal, 2016: Detection from Influenza-like Illness and Acute Flaccid Paralysis Surveillance

Following the 2014 outbreak, active surveillance of the EV-D68 has been implemented in many countries worldwide. Despite subsequent EV-D68 outbreaks (2014 and 2016) reported in many areas, EV-D68 circulation remains largely unexplored in Africa except in Senegal, where low levels of EV-D68 circulation were first noted during the 2014 outbreak. Here we investigate subsequent epidemiology of EV-D68 in Senegal from June to September 2016 by screening respiratory specimens from ILI and stool from AFP surveillance. EV-D68 was detected in 7.4% (44/596) of patients; 40 with ILI and 4 with AFP. EV-D68 detection was significantly more common in children under 5 years (56.8%, p = 0.016). All EV-D68 strains detected belonged to the newly defined subclade B3. This study provides the first evidence of EV-D68 B3 subclade circulation in Africa from patients with ILI and AFP during a 2016 outbreak in Senegal. Enhanced surveillance of EV-D68 is needed to better understand the epidemiology of EV-D68 in Africa.