Culture-Independent Discovery of Viroids by Deep Sequencing and Computational Algorithms

2021 ◽  
pp. 251-274
Author(s):  
Ali Raza ◽  
Shou-Wei Ding ◽  
Qingfa Wu
Keyword(s):  
Deep Sequencing ◽  
Computational Algorithms ◽  
Culture Independent

scholarly journals Detection of Emerging Vaccine-Related Polioviruses by Deep Sequencing

2017 ◽  
Vol 55 (7) ◽  
pp. 2162-2171 ◽  
Author(s):  
Malaya K. Sahoo ◽  
Marisa Holubar ◽  
ChunHong Huang ◽  
Alisha Mohamed-Hadley ◽  
Yuanyuan Liu ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Read Depth ◽  
Polio Eradication ◽  
Oral Poliovirus Vaccine ◽  
Genomic Region ◽  
Sample Collection ◽  
Asymptomatic Children ◽  
National Immunization ◽  
Sequencing Method ◽  
Culture Independent

ABSTRACTOral poliovirus vaccine can mutate to regain neurovirulence. To date, evaluation of these mutations has been performed primarily on culture-enriched isolates by using conventional Sanger sequencing. We therefore developed a culture-independent, deep-sequencing method targeting the 5′ untranslated region (UTR) and P1 genomic region to characterize vaccine-related poliovirus variants. Error analysis of the deep-sequencing method demonstrated reliable detection of poliovirus mutations at levels of <1%, depending on read depth. Sequencing of viral nucleic acids from the stool of vaccinated, asymptomatic children and their close contacts collected during a prospective cohort study in Veracruz, Mexico, revealed no vaccine-derived polioviruses. This was expected given that the longest duration between sequenced sample collection and the end of the most recent national immunization week was 66 days. However, we identified many low-level variants (<5%) distributed across the 5′ UTR and P1 genomic region in all three Sabin serotypes, as well as vaccine-related viruses with multiple canonical mutations associated with phenotypic reversion present at high levels (>90%). These results suggest that monitoring emerging vaccine-related poliovirus variants by deep sequencing may aid in the poliovirus endgame and efforts to ensure global polio eradication.

Revisiting bovine pyometra—New insights into the disease using a culture-independent deep sequencing approach

2015 ◽  
Vol 175 (2-4) ◽  
pp. 319-324 ◽  
Author(s):  
Lif Rødtness Vesterby Knudsen ◽  
Cecilia Christensen Karstrup ◽  
Hanne Gervi Pedersen ◽  
Jørgen Steen Agerholm ◽  
Tim Kåre Jensen ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Culture Independent ◽  
Deep Sequencing Approach
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