scholarly journals Molecular evolution and genetic diversity analysis of SFTS virus based on next-generation sequencing

2021 ◽  
Author(s):  
Aqian Li ◽  
Lin Liu ◽  
Wei Wu ◽  
Yang Liu ◽  
Xiaoxia Huang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Molecular Evolution ◽  
Diversity Analysis ◽  
Next Generation ◽  
Genetic Diversity Analysis ◽  
Generation Sequencing

scholarly journals Testing the genomic stability of the Brazilian yellow fever vaccine strain using next-generation sequencing data

2021 ◽  
Vol 11 (4) ◽  
pp. 20200063 ◽  
Author(s):  
Amanda Araújo Serrão de Andrade ◽  
André E. R. Soares ◽  
Luiz Gonzaga Paula de Almeida ◽  
Luciane Prioli Ciapina ◽  
Cristiane Pinheiro Pestana ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Yellow Fever ◽  
Vaccine Strain ◽  
Next Generation Sequencing Data ◽  
Diversity Analysis ◽  
Vaccine Production ◽  
Next Generation ◽  
Genetic Diversity Analysis ◽  
Generation Sequencing

The live attenuated yellow fever (YF) vaccine was developed in the 1930s. Currently, the 17D and 17DD attenuated substrains are used for vaccine production. The 17D strain is used for vaccine production by several countries, while the 17DD strain is used exclusively in Brazil. The cell passages carried out through the seed-lot system of vaccine production influence the presence of quasispecies causing changes in the stability and immunogenicity of attenuated genotypes by increasing attenuation or virulence. Using next-generation sequencing, we carried out genomic characterization and genetic diversity analysis between vaccine lots of the Brazilian YF vaccine, produced by BioManguinhos–Fiocruz, and used during 11 years of vaccination in Brazil. We present 20 assembled and annotated genomes from the Brazilian 17DD vaccine strain, eight single nucleotide polymorphisms and the quasispecies spectrum reconstruction for the 17DD vaccine, through a pipeline here introduced. The V2IDA pipeline provided a relationship between low genetic diversity, maintained through the seed lot system, and the confirmation of genetic stability of lots of the Brazilian vaccine against YF. Our study sets precedents for use of V2IDA in genetic diversity analysis and in silico stability investigation of attenuated viral vaccines, facilitating genetic surveillance during the vaccine production process.

Genetic diversity of Hepatitis C Virus in Pakistan using Next Generation Sequencing

2018 ◽  
Vol 108 ◽  
pp. 26-31 ◽  
Author(s):  
Sana Saleem ◽  
Amjad Ali ◽  
Bushra Khubaib ◽  
Madiha Akram ◽  
Zareen Fatima ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS)

PLoS ONE ◽  
2017 ◽  
Vol 12 (7) ◽  
pp. e0181279 ◽  
Author(s):  
Amanda D. Barbosa ◽  
Alexander W. Gofton ◽  
Andrea Paparini ◽  
Annachiara Codello ◽  
Telleasha Greay ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Phascolarctos Cinereus ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals Discovery of Bat Coronaviruses through Surveillance and Probe Capture-Based Next-Generation Sequencing

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Bei Li ◽  
Hao-Rui Si ◽  
Yan Zhu ◽  
Xing-Lou Yang ◽  
Danielle E. Anderson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Active Surveillance ◽  
Large Scale ◽  
Next Generation ◽  
High Genetic Diversity ◽  
High Background ◽  
Field Samples ◽  
Great Genetic Diversity ◽  
Generation Sequencing

ABSTRACT Coronaviruses (CoVs) of bat origin have caused two pandemics in this century. Severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV both originated from bats, and it is highly likely that bat coronaviruses will cause future outbreaks. Active surveillance is both urgent and essential to predict and mitigate the emergence of these viruses in humans. Next-generation sequencing (NGS) is currently the preferred methodology for virus discovery to ensure unbiased sequencing of bat CoVs, considering their high genetic diversity. However, unbiased NGS is an expensive methodology and is prone to missing low-abundance CoV sequences due to the high background level of nonviral sequences present in surveillance field samples. Here, we employ a capture-based NGS approach using baits targeting most of the CoV species. Using this technology, we effectively reduced sequencing costs by increasing the sensitivity of detection. We discovered nine full genomes of bat CoVs in this study and revealed great genetic diversity for eight of them. IMPORTANCE Active surveillance is both urgent and essential to predict and mitigate the emergence of bat-origin CoV in humans and livestock. However, great genetic diversity increases the chance of homologous recombination among CoVs. Performing targeted PCR, a common practice for many surveillance studies, would not reflect this diversity. NGS, on the other hand, is an expensive methodology and is prone to missing low-abundance CoV sequences. Here, we employ a capture-based NGS approach using baits targeting all CoVs. Our work demonstrates that targeted, cost-effective, large-scale, genome-level surveillance of bat CoVs is now highly feasible.

scholarly journals Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing

2020 ◽  
Vol 11 ◽  
Author(s):  
Fen Wu ◽  
Hao Sun ◽  
Shaoxiong Lu ◽  
Xiao Gou ◽  
Dawei Yan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Selection Signatures ◽  
Generation Sequencing
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