Montmayeur, A. | Search bioRxiv

bioRxiv2023

Glycochenodeoxycholic acid and ceramide suppress the antiviral effect of 25-hydroxycholesterol against human norovirus infection in human intestinal enteroids

The human intestinal enteroid (HIE) cell culture system with the support of glycine-conjugated bile acid glycochenodeoxycholic acid (GCDCA) and ceramide (C2) facilitate successful replication of several norovirus strains. Here we investigate how the presence of GCDCA/C2 impacts gene expression of norovirus-infected HIE and the impact of 25 hydroxycholesterol (25-HC), a key regulator of cholesterol homeostasis and bile acid production on norovirus replication. In absence of GCDCA/C2, 0.01 and 0.1 M 25-HC suppressed virus (GII.4 Sydney[P16]) replication by 1.3 log and 1.1 log respectively (p<0.05). In the presence of GCDCA/C2, 5 M 25-HC was required to achieve a 1 log decrease (p<0.05) in viral titers demonstrating that 25-HC restricts norovirus replication in HIE. RNA sequence analysis showed that during human norovirus infection, 25-HC downregulated expression of genes (CYP3A4, APOB, APOA1, and ABCG1) involved in cholesterol metabolism and transport as well as interferon stimulated genes such as ISG15 and IFIT1. GCDCA/C2 counteracts the suppressive effect of 25-HC expression of some genes related to these pathways including APOA4 and CYP27A1 however, other cholesterol genes such as APOA1 were further suppressed in the presence of GCDCA/C2. ImportanceNorovirus is the leading cause of epidemic and endemic acute gastroenteritis worldwide and currently, there are no effective therapeutic strategies against this highly contagious pathogen. Our study provides insights into the effect of bile during norovirus infection, highlight the role of the cholesterol/oxysterol pathways during human norovirus replication, and demonstrate the potential utility of oxysterols in developing norovirus therapeutics.

genetics↗

bioRxiv2019

Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

Next-generation sequencing is a powerful tool for virological surveillance. While Illumina(R) and Ion Torrent(R) sequencing platforms are used extensively for generating viral RNA genome sequences, there is limited data comparing different platforms. We evaluated the Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms using a panel of sixteen specimens containing picornaviruses and human caliciviruses (noroviruses and sapoviruses). The specimens were processed, using combinations of three library preparation and five sequencing kits, to assess the quality and completeness of assembled viral genomes, and an estimation of cost per sample to generate the data was calculated. The choice of library preparation kit and sequencing platform was found to impact the breadth of genome coverage and accuracy of consensus viral genomes. The Ion Torrent S5 outperformed the older Ion Torrent PGM platform in data quality and cost, and generated the highest proportion of reads for enterovirus D68 samples. However, indels at homopolymer regions impacted the accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., Ion Torrent 510 or Illumina MiSeq Nano V2), the cost per sample was lower on the MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 or Illumina MiSeq V2) the cost per sample was comparable. These findings suggest that the Ion Torrent S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of RNA viruses, each with specific advantages and tradeoffs.

microbiology↗