Near Full-Length Genome Sequences of Two Novel HIV-1 Recombinant Forms Detected in Henan Province, China

2016 ◽  
Vol 32 (7) ◽  
pp. 722-727 ◽  
Author(s):  
Tianyi Li ◽  
Guoqing Sun ◽  
Dijing Jia ◽  
Changrong Sun ◽  
Zhe Wang ◽  
...  
Keyword(s):  
Henan Province ◽  
Full Length ◽  
Genome Sequences ◽  
Full Length Genome ◽  
Hiv 1

Near-Full-Length Genome Sequences of a Novel HIV-1 Circulating Recombinant Form, CRF01_AE/B′/C (CRF78_cpx), in Yunnan, China

2016 ◽  
Vol 32 (6) ◽  
pp. 601-606 ◽  
Author(s):  
Yindi Song ◽  
Yue Feng ◽  
Zhijiang Miao ◽  
Binghui Wang ◽  
Ming Yang ◽  
...  
Keyword(s):  
Full Length ◽  
Recombinant Form ◽  
Genome Sequences ◽  
Full Length Genome ◽  
Hiv 1

scholarly journals Full-length genome sequences of Estonian HIV-1 CRF06 and Eastern-European subtype A1 recombinant forms

2014 ◽  
Vol 14 (S4) ◽  
Author(s):  
Radko Avi ◽  
Kristi Huik ◽  
Merit Pauskar ◽  
Eveli Kallas ◽  
Ene-Ly Jõgeda ◽  
...  
Keyword(s):  
Full Length ◽  
Eastern European ◽  
Genome Sequences ◽  
Full Length Genome ◽  
European Subtype ◽  
Hiv 1

scholarly journals Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences

2002 ◽  
Vol 83 (1) ◽  
pp. 107-119 ◽  
Author(s):  
Michael M. Thomson ◽  
Elena Delgado ◽  
Isabel Herrero ◽  
María Luisa Villahermosa ◽  
Elena Vázquez-de Parga ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Full Length ◽  
Common Ancestry ◽  
Genome Sequences ◽  
Recombinant Viruses ◽  
Immunodeficiency Virus ◽  
Relationship Of ◽  
Full Length Genome ◽  
Hiv 1

The findings that BF intersubtype recombinant human immunodeficiency type 1 viruses (HIV-1) with coincident breakpoints in pol are circulating widely in Argentina and that non-recombinant F subtype viruses have failed to be detected in this country were reported recently. To analyse the mosaic structures of these viruses and to determine their phylogenetic relationship, near full-length proviral genomes of eight of these recombinant viruses were amplified by PCR and sequenced. Intersubtype breakpoints were analysed by bootscanning and examining the signature nucleotides. Phylogenetic relationships were determined with neighbour-joining trees. Five viruses, each with predominantly subtype F genomes, exhibited mosaic structures that were highly similar. Two intersubtype breakpoints were shared by all viruses and seven by the majority. Of the consensus breakpoints, all nine were present in two viruses, which exhibited identical recombinant structures, and four to eight breakpoints were present in the remaining viruses. Phylogenetic analysis of partial sequences supported both a common ancestry, at least in part of their genomes, for all recombinant viruses and the phylogenetic relationship of F subtype segments with F subtype viruses from Brazil. A common ancestry of the recombinants was supported also by the presence of shared signature amino acids and nucleotides, either unreported or highly unusual in F and B subtype viruses. These results indicate that HIV-1 BF recombinant viruses with diverse mosaic structures, including a circulating recombinant form (which are widespread in Argentina) derive from a common recombinant ancestor and that F subtype segments of these recombinants are related phylogenetically to the F subtype viruses from Brazil.

Tracing the origin and history of HIV-1 subtype B′ epidemic by near full-length genome analyses

AIDS ◽  
2012 ◽  
Vol 26 (7) ◽  
pp. 877-884 ◽  
Author(s):  
Zhe Li ◽  
Xiang He ◽  
Zhe Wang ◽  
Hui Xing ◽  
Fan Li ◽  
...  
Keyword(s):  
Full Length ◽  
Subtype B ◽  
History Of ◽  
Genome Analyses ◽  
Full Length Genome ◽  
Hiv 1

scholarly journals NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2577
Author(s):  
Imogen A. Wright ◽  
Kayla E. Delaney ◽  
Mary Grace K. Katusiime ◽  
Johannes C. Botha ◽  
Susan Engelbrecht ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Cost Effective ◽  
Full Length ◽  
Sequencing Error ◽  
Consensus Building ◽  
Genome Sequences ◽  
Bioinformatics Pipeline ◽  
Oxford Nanopore ◽  
Single Genome ◽  
Hiv 1

HIV-1 proviral single-genome sequencing by limiting-dilution polymerase chain reaction (PCR) amplification is important for differentiating the sequence-intact from defective proviruses that persist during antiretroviral therapy (ART). Intact proviruses may rebound if ART is interrupted and are the barrier to an HIV cure. Oxford Nanopore Technologies (ONT) sequencing offers a promising, cost-effective approach to the sequencing of long amplicons such as near full-length HIV-1 proviruses, but the high diversity of HIV-1 and the ONT sequencing error render analysis of the generated data difficult. NanoHIV is a new tool that uses an iterative consensus generation approach to construct accurate, near full-length HIV-1 proviral single-genome sequences from ONT data. To validate the approach, single-genome sequences generated using NanoHIV consensus building were compared to Illumina® consensus building of the same nine single-genome near full-length amplicons and an average agreement of 99.4% was found between the two sequencing approaches.

scholarly journals Full-Length Genome Sequences of Recombinant and Nonrecombinant Sympatric Strains of Rice yellow mottle virus from Western Kenya

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
Antony Kigaru Adego ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
Benard Mukoye ◽  
Denis Fargette ◽  
...  
Keyword(s):  
Full Length ◽  
Mottle Virus ◽  
Rice Yellow Mottle Virus ◽  
Genome Sequences ◽  
Western Kenya ◽  
Yellow Mottle ◽  
Full Length Genome

ABSTRACT Five isolates of Rice yellow mottle virus from western Kenya were fully sequenced. One isolate of strain S4lv had been collected in 1966. Two isolates belonged to the emerging strain S4ug recently described in Uganda. Two isolates collected in 2012 are putative recombinants between the S4lv and S4ug strains.

scholarly journals Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial

2020 ◽  
Vol 222 (10) ◽  
pp. 1670-1680
Author(s):  
Vlad Novitsky ◽  
Melissa Zahralban-Steele ◽  
Sikhulile Moyo ◽  
Tapiwa Nkhisang ◽  
Dorcas Maruapula ◽  
...  
Keyword(s):  
Hiv Transmission ◽  
Full Length ◽  
Treatment As Prevention ◽  
People Living With Hiv ◽  
Genome Sequences ◽  
Transmission Networks ◽  
Combination Prevention ◽  
Prevention Project ◽  
Prevention Interventions ◽  
Hiv 1

Abstract Background Phylogenetic mapping of HIV-1 lineages circulating across defined geographical locations is promising for better understanding HIV transmission networks to design optimal prevention interventions. Methods We obtained near full-length HIV-1 genome sequences from people living with HIV (PLWH), including participants on antiretroviral treatment in the Botswana Combination Prevention Project, conducted in 30 Botswana communities in 2013–2018. Phylogenetic relationships among viral sequences were estimated by maximum likelihood. Results We obtained 6078 near full-length HIV-1C genome sequences from 6075 PLWH. We identified 984 phylogenetically distinct HIV-1 lineages (molecular HIV clusters) circulating in Botswana by mid-2018, with 2–27 members per cluster. Of these, dyads accounted for 62%, approximately 32% (n = 316) were found in single communities, and 68% (n = 668) were spread across multiple communities. Men in clusters were approximately 3 years older than women (median age 42 years, vs 39 years; P < .0001). In 65% of clusters, men were older than women, while in 35% of clusters women were older than men. The majority of identified viral lineages were spread across multiple communities. Conclusions A large number of circulating phylogenetically distinct HIV-1C lineages (molecular HIV clusters) suggests highly diversified HIV transmission networks across Botswana communities by 2018.

scholarly journals Near Full-Length Genome Identification of a Novel HIV-1 Recombinant Form (CRF01_AE/B′/C) Among Heterosexuals in Jilin, China

2014 ◽  
Vol 30 (7) ◽  
pp. 695-700 ◽  
Author(s):  
Xingguang Li ◽  
Chuanyi Ning ◽  
Yanli Chen ◽  
Yi Feng ◽  
Min Wei ◽  
...  
Keyword(s):  
Full Length ◽  
Recombinant Form ◽  
Full Length Genome ◽  
Hiv 1

Full-Length Genome Analysis of HIV-1 Subtype C Utilizing CXCR4 and Intersubtype Recombinants Isolated in South Africa

2002 ◽  
Vol 18 (12) ◽  
pp. 879-886 ◽  
Author(s):  
Maria A. Papathanasopoulos ◽  
Tonie Cilliers ◽  
Lynn Morris ◽  
John L. Mokili ◽  
William Dowling ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Analysis ◽  
Full Length ◽  
Subtype C ◽  
Full Length Genome ◽  
Hiv 1

scholarly journals Natural infection of Atlantic salmon (Salmo salar L.) with salmonid alphavirus 3 generates numerous viral deletion mutants

2013 ◽  
Vol 94 (9) ◽  
pp. 1945-1954 ◽  
Author(s):  
Elin Petterson ◽  
Marit Stormoen ◽  
Øystein Evensen ◽  
Aase B. Mikalsen ◽  
Øyvind Haugland
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Natural Infection ◽  
Sequence Divergence ◽  
Heart Tissue ◽  
Full Length ◽  
Deletion Mutants ◽  
Genome Sequences ◽  
Pancreas Disease ◽  
Full Length Genome

Salmon pancreas disease virus (SPDV) also referred to as salmonid alphavirus (SAV) is a virus causing pancreas disease in Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss). Although the virus causes an economically important disease, relatively few full-length genome sequences of SAV strains are currently available. Here, we report full-length genome sequences of nine SAV3 strains from sites farming Atlantic salmon geographically spread along the Norwegian coastline. The virus genomes were sequenced directly from infected heart tissue, to avoid culture selection bias. Sequence analysis confirmed a high level of sequence identity within SAV3 strains, with a mean nucleotide diversity of 0.11 %. Sequence divergence was highest in 6K and E2, while lowest in the capsid protein and the non-structural proteins (nsP4 and nsP2). This study reports for the first time that numerous defective viruses containing genome deletions are generated during natural infection with SAV. Deletions occurred in all virus strains and were not distributed randomly throughout the genome but instead tended to aggregate in certain areas. We suggest imprecise homologous recombination as an explanation for generation of defective viruses with genome deletions. The presence of such viruses, provides a possible explanation for the difficulties in isolating SAV in cell culture. Primary virus isolation was successfully achieved for only two of eight strains, despite extensive attempts using three different cell lines. Both SAV isolates were easily propagated further and concomitant viral deletion mutants present in clinically infected heart tissue were maintained following serial passage in CHH-1 cells.

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