scholarly journals Enhanced detection of viral diversity using partial and near full-length genomes of human immunodeficiency virus Type 1 provirus deep sequencing data from recently infected donors at four blood centers in Brazil

Transfusion ◽  
2014 ◽  
Vol 55 (5) ◽  
pp. 980-990 ◽  
Author(s):  
Rodrigo Pessôa ◽  
Jaqueline Tomoko Watanabe ◽  
Paula Calabria ◽  
Cecilia Salete Alencar ◽  
Paula Loureiro ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Deep Sequencing ◽  
Full Length ◽  
Viral Diversity ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Immunodeficiency Virus

Full-Length Genome Analysis of Human Immunodeficiency Virus Type 1 Subtype C in Brazil

2006 ◽  
Vol 22 (2) ◽  
pp. 171-176 ◽  
Author(s):  
Sabri Sanabani ◽  
Walter Kleine Neto ◽  
Dercy José De Sa Filho ◽  
Ricardo Sobhie Diaz ◽  
Patrícia Munerato ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Genome Analysis ◽  
Full Length ◽  
Subtype C ◽  
Immunodeficiency Virus ◽  
Full Length Genome

Full-Length Sequence of an Ethiopian Human Immunodeficiency Virus Type 1 (HIV-1) Isolate of Genetic Subtype C

1996 ◽  
Vol 12 (14) ◽  
pp. 1329-1339 ◽  
Author(s):  
MIKA O. SALMINEN ◽  
BO JOHANSSON ◽  
ANDERS SÖNNERBORG ◽  
SEYOUM AYEHUNIE ◽  
DEANNA GOTTE ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Full Length ◽  
Subtype C ◽  
Genetic Subtype ◽  
Immunodeficiency Virus ◽  
Full Length Sequence ◽  
Hiv 1

scholarly journals Using Primer-ID Deep Sequencing to Detect Recent Human Immunodeficiency Virus Type 1 Infection

2018 ◽  
Vol 218 (11) ◽  
pp. 1777-1782 ◽  
Author(s):  
Ann M Dennis ◽  
Shuntai Zhou ◽  
Christopher J Sellers ◽  
Emily Learner ◽  
Marc Potempa ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Deep Sequencing ◽  
Immunodeficiency Virus

scholarly journals Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated ‘subtype I’, reveals a unique complex A/G/H/K/? mosaic pattern

2001 ◽  
Vol 82 (3) ◽  
pp. 575-580 ◽  
Author(s):  
D. Paraskevis ◽  
M. Magiorkinis ◽  
A. M. Vandamme ◽  
L. G. Kostrikis ◽  
A. Hatzakis
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Genomic Organization ◽  
Full Length ◽  
Mosaic Pattern ◽  
Infected Population ◽  
Immunodeficiency Virus ◽  
Hiv 1

Human immunodeficiency virus type 1 (HIV-1) has been classified into three main groups and 11 distinct subtypes. Moreover, several circulating recombinant forms (CRFs) of HIV-1 have been recently documented to have spread widely causing extensive HIV-1 epidemics. A subtype, initially designated I (CRF04_cpx), was documented in Cyprus and Greece and was found to comprise regions of sequence derived from subtypes A and G as well as regions of unclassified sequence. Re-analysis of the three full-length CRF04_cpx sequences that were available revealed a mosaic genomic organization of unique complexity comprising regions of sequence from at least five distinct subtypes, A, G, H, K and unclassified regions. These strains account for approximately 2% of the total HIV-1-infected population in Greece, thus providing evidence of the great capability of HIV-1 to recombine and produce highly divergent strains which can be spread successfully through different infection routes.

scholarly journals Interaction of YB-1 with human immunodeficiency virus type 1 Tat and TAR RNA modulates viral promoter activity

1999 ◽  
Vol 80 (10) ◽  
pp. 2629-2638 ◽  
Author(s):  
Sameer A. Ansari ◽  
Mahmut Safak ◽  
Gary L. Gallia ◽  
Bassel E. Sawaya ◽  
Shohreh Amini ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Rna Binding ◽  
Regulatory Element ◽  
Binding Activity ◽  
Full Length ◽  
Immunodeficiency Virus ◽  
Hiv 1

Transcriptional regulation of the human immunodeficiency virus type 1 (HIV-1) genome is mediated by viral and cellular factors. TAR, an unusual RNA regulatory element with a stem–bulge–loop structure at the 5′ ends of all nascent viral transcripts is critical for HIV-1 transcription. TAR is the target for Tat, a viral transcription factor encoded early in the HIV-1 life-cycle and essential for gene expression. Evidence demonstrating the interaction of a cellular ssDNA/RNA binding protein, YB-1, with TAR through a region which is important for Tat interaction is presented. Interestingly, results from protein–protein interaction studies revealed that YB-1 can also form a complex with Tat. Results from mapping experiments suggest that while the region spanning aa 125–203 within YB-1 is essential for its association with TAR, a truncated YB-1 spanning aa 1–125 can weakly bind to Tat. Functionally, overexpression of full-length YB-1 enhanced Tat-induced activation of the HIV-1 minimal promoter containing TAR sequences, whereas mutant YB-1 with no ability to bind to Tat and TAR failed to affect Tat-mediated activation. Expression of mutant YB-1(1–125), which binds to Tat but not RNA, decreased Tat- mediated enhancement of virus transcription. These observations suggest that while full-length YB-1 may function as a facilitator and, by interaction with both Tat and TAR, increase the level of Tat:TAR association, mutant YB-1 with no TAR binding activity, by complexing with Tat, may prevent Tat interaction with TAR. The importance of these findings in light of the proposed mechanism of Tat function is discussed.

scholarly journals Sustained G→A hypermutation during reverse transcription of an entire human immunodeficiency virus type 1 strain Vau group O genome

2002 ◽  
Vol 83 (4) ◽  
pp. 801-805 ◽  
Author(s):  
Jean-Pierre Vartanian ◽  
Michel Henry ◽  
Simon Wain-Hobson
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Reverse Transcription ◽  
Full Length ◽  
Minus Strand ◽  
Immunodeficiency Virus

Two full-length human immunodeficiency virus type 1 O sequences are described, one of which was hypermutated in all regions of the genome. This indicates that the intracellular [dTTP]/[dCTP] bias conducive to G→A hypermutation may be sustained throughout the synthesis of minus-strand DNA. In turn, this suggests the possibility of mutation of host sequences.

scholarly journals Molecular Cloning and Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Subtype C: a Set of 23 Full-Length Clones from Botswana

1999 ◽  
Vol 73 (5) ◽  
pp. 4427-4432 ◽  
Author(s):  
Vladimir A. Novitsky ◽  
Monty A. Montano ◽  
Mary F. McLane ◽  
Boris Renjifo ◽  
Fredrik Vannberg ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Southern Africa ◽  
Full Length ◽  
Subtype C ◽  
Subtype B ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT To better understand the virological aspect of the expanding AIDS epidemic in southern Africa, a set of 23 near-full-length clones of human immunodeficiency virus type 1 (HIV-1) representing eight AIDS patients from Botswana were sequenced and analyzed phylogenetically. All study viruses from Botswana belonged to HIV-1 subtype C. The interpatient diversity of the clones from Botswana was higher than among full-length isolates of subtype B or among a set of full-length HIV-1 genomes of subtype C from India (mean value of 9.1% versus 6.5 and 4.3%, respectively; P < 0.0001 for both comparisons). Similar results were observed in all genes across the entire viral genome. We suggest that the high level of HIV-1 diversity might be a typical feature of the subtype C epidemic in southern Africa. The reason or reasons for this diversity are unclear, but may include an altered replication efficiency of HIV-1 subtype C and/or the multiple introduction of different subtype C viruses.

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