Queiroz, C. | Search bioRxiv

bioRxiv2025

The development and validation of long-read ITS-1/5.8S/ITS-2 nemabiome metabarcoding using Oxford Nanopore Technologies (ONT) sequencing for ovine gastrointestinal nematodes and the design of primers suitable for its direct application to fecal DNA.

ITS-2 rRNA nemabiome metabarcoding is increasingly used to characterize gastrointestinal nematode (GIN) communities. While powerful, current approaches have some limitations in their flexibility and applicability to smaller-scale studies and diagnostic use. The short read lengths provided by the Illumina platform may lack discriminatory power for some closely related species and also pose a challenge for new marker selection and primer design. To address these challenges, we have developed ITS-1/5.8S/ITS-2 rRNA Oxford Nanopore Technologies (ONT) long-read metabarcoding for ovine gastrointestinal nematodes. Samples from two previous field studies, from UK and western Canadian sheep farms were used. ITS-1/5.8S/ITS-2 long-read metabarcoding showed strong concordance with prior ITS-2 data for the major GIN species in both datasets, with minor discrepancies for some low abundance taxa mainly due to differences in reference sequence database representation. We also used the PrimerTC tool to design a new primer pair, EC1 and EC2, to minimize the amplification of off-target fungal sequences derived from fecal DNA and maximize the nematode sequence read depth when ONT ITS-1/5.8S/ITS-2 metabarcoding was applied directly to ovine fecal stool DNA. In summary, ITS-1/5.8S/ITS-2 ONT long-read nemabiome metabarcoding showed good agreement with ITS-2 metabarcoding and the use of primer pair EC1/EC2 should make the approach more tolerant of fecal contamination of parasite material, with the potential for direct application to ovine fecal DNA. Overall, these new developments should make nemabiome metabarcoding more accessible, discriminating, and flexible for both research and diagnostic applications.

molecular biology↗

bioRxiv2018

Beyond members of the Flaviviridae family, sofosbuvir also inhibits chikungunya virus replication

Chikungunya virus (CHIKV) causes a febrile disease associated with chronic arthralgia, which may progress to neurological impairment. Chikungunya fever (CF) is a consolidated public health problem, in tropical and subtropical regions of the world, where control of CHIKV vector, mosquitos of the Aedes genus, failed. Since there is no vaccine or specific treatment against CHIKV, infected patients receive only palliative care to alleviate pain and arthralgia. Thus, drug repurposing is necessary to identify antivirals against CHIKV. Recently, the structure and activity of CHIKV RNA polymerase was partially resolved, revealing similar aspects with the enzyme counterparner on other positive sense RNA viruses, such as members of the Flaviviridae family. We then evaluated if sofosbuvir, clinically approved against hepatitis C virus RNA polymerase, which also aims to dengue, Zika and yellow fever viruses replication, would inhibit CHIKV replication. Indeed, sofosbuvir was 5-times more selective in inhibiting CHIKV production in human hepatoma cells than ribavirin, a pan-antiviral drug. Although CHIKV replication in human induced pluripotent stem cell (iPS)-derived astrocytes was less sensitive to sofosbuvirs, compared to hepatoma cells - this drug still impaired virus production and cell death in a MOI-dependent manner. Sofosbuvir also exhibited antiviral activity in vivo, by preventing CHIKV-induced paw oedeme in adult mice, at 20 mg/kg/day, and mortality on neonate mice model, at 40 and 80 mg/kg/day. Our data demonstrates that a prototypic alphavirus, CHIKV, is also susceptible to sofosbuvir. Since this is a clinically approved drug, it could pave the way to become a therapeutic option against CF.

microbiology↗