EV-D68 is a single-stranded positive-sense RNA virus belonging to the Enterovirus genus of the Picornaviridae family. EV-D68 infection usually leads to severe respiratory illness and has recently been reported to be linked to the development of the neurogenic disease known as acute flaccid myelitis (AFM), mostly in children. This phenomenon suggests a potential for EV-D68 to induce nervous system disease, arousing widespread concern among health authorities and the public. Despite the fact that EV-D68-associated infection was previously considered infrequent, since 2005 it has undergone a worldwide burst of growth in the USA, Asia, and Europe.

Several FDA approved drugs were found to target non-structural proteins of enterovirus making them potential antiviral agents. Fluoxetine (Prozac) was found to target EV-D68 protein 2C interfering with viral RNA replication. However, fluoxetine was proven to be ineffective in preventing the neurological effects of EV-D68. Telaprevir, a FDA-approved drug used for treatment of hepatitis C viral infection, was recently found to target EV-D68 2A protease (2Apro) which functions as a viral protease cleaving a peptide sequence corresponding to the VP1-2A polyprotein junction. The binding of telaprevir potently inhibits EV-D68 enzymatic activity making the virus non-functional.

Datasets and Data Upload for Phylogenetic Analysis

Phylogenetic Analysis of EVD-68 based on NGS data using T-Bioinfo Server

The data for this project was obtained from the National Centre for Biotechnology Information public domain. NGS data was obtained from the NCBI SRA database, and whole genome sequences from NCBI Nucleotide database.

Datasets

For this study, Swedish NGS data (SRA files) of EV-D68 samples from years 2014, 2016 and 2018 were used [Dyrdak et al, 2019]. Also, several EV-D68 genomes of known clades from the USA were used.

Links for the Data used in the project

1. SRA-Run Table: https://raw.githubusercontent.com/pine-bio-support/EV-D68-project/main/SRA_run-table.txt

2. Reference Genome (Genbank format): https://raw.githubusercontent.com/pine-bio-support/EV-D68-project/main/KP745764_ref_genome.gb

3. Outgroup1-1962 (Genbank format): https://raw.githubusercontent.com/pine-bio-support/EV-D68-project/main/NC_038308_outgroup-1962.gb

4. Outgroup2-2013 (Genbank format): https://raw.githubusercontent.com/pine-bio-support/EV-D68-project/main/KP100794_outgroup2.gb

5. Sequence information file: https://raw.githubusercontent.com/pine-bio-support/EV-D68-project/main/Sequence-info.csv

This tree has three clear distinct clades for the samples from three different outbreaks ( 2014, 2016 and 2018). Further, we observed there are two clades for 2016 outbreak [Group2], where in one clade, 7 haplotypes are grouped together and in another clade, two haplotypes grouped together. Fermon (outhroup -1962) has a distinct smaller clade. Interestingly, the clade of another outgroup (2013) is closer to the clade of Group 1 samples (2014). Further, we observed, there are 9 haplotypes for group 2, 7 haplotypes for each group 1 and group 3.

Sun et al, 2019 hypothesized that the EV-D68 acquired pathogenicity after the Fermon strain was isolated. But when exactly? In 2014 only very few or no cases of AFM-associated EV-D68 infection occurred, and in 2016 and 2018 the number of AFM cases have risen dramatically. It is considered the EV-D68 in 2016 and 2018 has acquired neurovirulence of AFM, and Sun et al, 2019 has identified six mutations possibly responsible for the condition.

To learn more about the project, visit: https://learn.omicslogic.com/courses/course/project-04-ev-d68-and-acute-flaccid-myelitis-in-kids 

For any questions, mail us at support@pine.bio