Within Host Evolution of Malaria Parasites Revealed by Single Genome Sequencing

2020 ◽  
Author(s):  
Aliou Dia ◽  
Catherine Jett ◽  
Simon G. Trevino ◽  
Cindy S. Chu ◽  
Kanlaya Sriprawat ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Malaria Parasites ◽  
Single Genome ◽  
Host Evolution

Single-genome sequencing reveals within-host evolution of human malaria parasites

2021 ◽  
Author(s):  
Aliou Dia ◽  
Catherine Jett ◽  
Simon G. Trevino ◽  
Cindy S. Chu ◽  
Kanlaya Sriprawat ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Malaria Parasites ◽  
Human Malaria ◽  
Single Genome ◽  
Host Evolution

scholarly journals Assessing routes of hepatitis C transmission in HIV-infected men who have sex with men using single genome sequencing

PLoS ONE ◽  
2020 ◽  
Vol 15 (7) ◽  
pp. e0235237
Author(s):  
Hui Li ◽  
Kristen M. Marks ◽  
Andrew H. Talal ◽  
Wouter O. van Seggelen ◽  
Bisher Akil ◽  
...  
Keyword(s):  
Hepatitis C ◽  
Genome Sequencing ◽  
Single Genome ◽  
Sex With Men

scholarly journals Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Bhavna Hora ◽  
Naila Gulzar ◽  
Yue Chen ◽  
Konstantinos Karagiannis ◽  
Fangping Cai ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Vaccine Development ◽  
Consensus Sequence ◽  
Cost Effective ◽  
Recombination Analysis ◽  
Genome Sequences ◽  
Single Genome ◽  
Hiv 1

ABSTRACT High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).

scholarly journals Amino Acid Prevalence of HIV-1 pol Mutations by Direct Polymerase Chain Reaction and Single Genome Sequencing

2019 ◽  
Vol 35 (10) ◽  
pp. 924-929 ◽  
Author(s):  
Philip L. Tzou ◽  
Soo-Yon Rhee ◽  
Robert W. Shafer
Keyword(s):  
Polymerase Chain Reaction ◽  
Amino Acid ◽  
Genome Sequencing ◽  
Chain Reaction ◽  
Direct Polymerase Chain Reaction ◽  
Single Genome ◽  
Polymerase Chain ◽  
Hiv 1

scholarly journals Real time, field-deployable whole genome sequencing of malaria parasites using nanopore technology

2020 ◽  
Author(s):  
Zahra Razook ◽  
Somya Mehra ◽  
Brittany Gilchrist ◽  
Digjaya Utama ◽  
Dulcie Lautu-Gumal ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Real Time ◽  
Genome Sequencing ◽  
Error Rates ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Virulence Determinants ◽  
Malaria Parasites ◽  
Additional Information ◽  
Natural Isolates

ABSTRACTMalaria parasite genomes have been generated predominantly using short read sequencing technology which can be slow, requires advanced laboratory training and does not adequately interrogate complex genomic regions that harbour important malaria virulence determinants. The portable Oxford Nanopore Technologies MinION platform generates long reads in real time and may overcome these limitations. We present compelling evidence that Nanopore sequencing delivers valuable additional information for malaria parasites with comparable data fidelity for single nucleotide variant (SNV) calls, compared to standard Illumina whole genome sequencing. We demonstrate this through sequencing of pure Plasmodium falciparum DNA, mock infections and natural isolates. Nanopore has low error rates for haploid SNV genotyping and identifies structural variants (SVs) not detected with short reads. Nanopore genomes are directly comparable to publically available genomes and produce high quality end to end chromosome assemblies. Nanopore sequencing will expedite genomic surveillance of malaria and provide new insights into parasite genome biology.

scholarly journals Molecular Mechanisms of HIV Type 1 Prophylaxis Failure Revealed by Single-Genome Sequencing

2013 ◽  
Vol 208 (10) ◽  
pp. 1598-1603 ◽  
Author(s):  
Hui Li ◽  
Lily Blair ◽  
Yalu Chen ◽  
Gerald Learn ◽  
Katja Pfafferott ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Molecular Mechanisms ◽  
Single Genome ◽  
Hiv Type 1

scholarly journals Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations

2010 ◽  
Vol 168 (1-2) ◽  
pp. 114-120 ◽  
Author(s):  
Michael R. Jordan ◽  
Mary Kearney ◽  
Sarah Palmer ◽  
Wei Shao ◽  
Frank Maldarelli ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Pcr Cloning ◽  
Single Genome ◽  
Hiv 1

scholarly journals Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Thomas D. Otto ◽  
Julian C. Rayner ◽  
Ulrike Böhme ◽  
Arnab Pain ◽  
Natasha Spottiswoode ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Malaria Parasites
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