Retroviridae Lentivirus

The family Retroviridae comprises a large number of enveloped, spherical to pleomorphic viruses with a linear, positive-sense, single-stranded RNA genome of 7 – 11 kb and a size of 80 – 100 nm. These viruses are furthermore classified into 2 subfamilies and 7 genera.

Their common characteristic which is represented in the name of the family is the enzyme reverse transcriptase. It enables the virus to reverse the flow of the genetic information from RNA to DNA. During the replication cycle, the ssRNA(+) is copied into dsDNA which is integrated into the cell’s genome (=provirus). Retroviruses are known to cause a wide range of diseases in both humans and many animal species, especially immunodeficiencies and tumours.

We are currently involved in sequencing projects considering the Human immunodeficiency virus (HIV), the causative agent of the ongoing acquired immune deficiency syndrome (AIDS) pandemic.

Data Downloads

This project is ongoing and data for this organism will be made available in due course.

[Genome Research Limited]

In collaboration with Myra McClure & Jonathan Weber (Imperial College London), we are involved in the SPARTAC study (Short Pulse Anti Retroviral Therapy at HIV Seroconversion) funded by the Wellcome Trust. It is a randomised-controlled trial comparing three different strategies of intervention in patients recently infected with HIV, i.e. (i) Long Course combination Anti-Retroviral Therapy (LCART) for 48 weeks, (ii) Short Course combination Anti-Retroviral Therapy (SCART) for 12 weeks and (iii) No Anti-Retroviral Therapy. The main objective is to determine whether treatment at primary infection for a limited duration delays damage to the immune system and prolongs time to initiation of long-term anti-HIV therapy. The CD4 cell counts as well as disease progression and the development of AIDS events will be monitored.

At the Sanger Institute, we are performing deep sequencing of the highly variable V3 region of the envelope gene using Roche/454 technology. The obtained very deep coverage enables us to identify minor variants. We will compare the sequence diversity before and after treatment within each patient and between groups to investigate whether the intensity of selection has an impact on the viral genetic diversity.

More information about the study can be found here

We are also working with Deenan Pillay (University College London) to generate whole genome sequences of diverse HIV strains from the UK isolated from the 1980’s until today. Phylogenetic analysis will be conducted to estimate evolution rates and to measure the impact of selective pressures (e.g. highly active antiretroviral therapy, humane restriction factors) on the unprecedented genetic diversity of this virus.

Published Genome Data

The reference sequence for the Human immunodeficiency virus 1 can be found here

Studies

Bridging the Evolution and Epidemiology of HIV in Europe

Sample

Strain

Run Accession

BEEHIVE5514945BEE0524-1EGAR00001135484
BEEHIVE5514944BEE0523-1EGAR00001143171
BEEHIVE5514944BEE0523-1EGAR00001135483
BEEHIVE5514943BEE0522-1EGAR00001135482
BEEHIVE5514943BEE0522-1EGAR00001143170
BEEHIVE5514942BEE0521-1EGAR00001135481
BEEHIVE5514942BEE0521-1EGAR00001143169
BEEHIVE5514941BEE0520-1EGAR00001135480
BEEHIVE5514941BEE0520-1EGAR00001143168
BEEHIVE5514940BEE0519-1EGAR00001135479
BEEHIVE5514940BEE0519-1EGAR00001143167
BEEHIVE5514939BEE0518-1EGAR00001143166
BEEHIVE5514939BEE0518-1EGAR00001135478
BEEHIVE5514938BEE0517-1EGAR00001143165
BEEHIVE5514938BEE0517-1EGAR00001135477
BEEHIVE5514937BEE0516-1EGAR00001143164
BEEHIVE5514937BEE0516-1EGAR00001135476
BEEHIVE5514936BEE0515-1EGAR00001143163
BEEHIVE5514936BEE0515-1EGAR00001135475
BEEHIVE5514935BEE0514-1EGAR00001143162
BEEHIVE5514935BEE0514-1EGAR00001135474
BEEHIVE5514934BEE0513-1EGAR00001143161
BEEHIVE5514934BEE0513-1EGAR00001135473
BEEHIVE5514933BEE0512-1EGAR00001135472
BEEHIVE5514933BEE0512-1EGAR00001143160
BEEHIVE5514932BEE0511-1EGAR00001135471
BEEHIVE5514932BEE0511-1EGAR00001143159
BEEHIVE5514931BEE0510-1EGAR00001143158
BEEHIVE5514931BEE0510-1EGAR00001135470
BEEHIVE5514930BEE0509-1EGAR00001143157
BEEHIVE5514930BEE0509-1EGAR00001135469
BEEHIVE5514929BEE0508-1EGAR00001143156
BEEHIVE5514929BEE0508-1EGAR00001135468
BEEHIVE5514928BEE0507-1EGAR00001143155
BEEHIVE5514928BEE0507-1EGAR00001135467
BEEHIVE5514927BEE0506-1EGAR00001143154
BEEHIVE5514927BEE0506-1EGAR00001135466
BEEHIVE5514926BEE0505-1EGAR00001135465
BEEHIVE5514926BEE0505-1EGAR00001143153
BEEHIVE5514925BEE0504-1EGAR00001143152
BEEHIVE5514925BEE0504-1EGAR00001135464
BEEHIVE5514924BEE0503-1EGAR00001135463
BEEHIVE5514924BEE0503-1EGAR00001143151
BEEHIVE5514923BEE0502-1EGAR00001135462
BEEHIVE5514923BEE0502-1EGAR00001143150
BEEHIVE5514922BEE0501-1EGAR00001143149
BEEHIVE5514922BEE0501-1EGAR00001135461
BEEHIVE5514921BEE0500-1EGAR00001135460
BEEHIVE5514921BEE0500-1EGAR00001143148
BEEHIVE5514920BEE0499-1EGAR00001135459
BEEHIVE5514920BEE0499-1EGAR00001143147
BEEHIVE5514919BEE0498-1EGAR00001143146
BEEHIVE5514919BEE0498-1EGAR00001135458
BEEHIVE5514918BEE0497-1EGAR00001135457
BEEHIVE5514918BEE0497-1EGAR00001143145
BEEHIVE5514917BEE0496-1EGAR00001143144
BEEHIVE5514917BEE0496-1EGAR00001135456
BEEHIVE5514916BEE0495-1EGAR00001143143
BEEHIVE5514916BEE0495-1EGAR00001135455
BEEHIVE5514915BEE0494-1EGAR00001143142
BEEHIVE5514915BEE0494-1EGAR00001135454
BEEHIVE5514914BEE0493-1EGAR00001135453
BEEHIVE5514914BEE0493-1EGAR00001143141
BEEHIVE5514913BEE0492-1EGAR00001143140
BEEHIVE5514913BEE0492-1EGAR00001135452
BEEHIVE5514912BEE0491-1EGAR00001143139
BEEHIVE5514912BEE0491-1EGAR00001135451
BEEHIVE5514911BEE0490-1EGAR00001143138
BEEHIVE5514911BEE0490-1EGAR00001135450
BEEHIVE5514910BEE0489-1EGAR00001143137
BEEHIVE5514910BEE0489-1EGAR00001135449
BEEHIVE5514909BEE0488-1EGAR00001143136
BEEHIVE5514909BEE0488-1EGAR00001135448
BEEHIVE5514908BEE0487-1EGAR00001135447
BEEHIVE5514908BEE0487-1EGAR00001143135
BEEHIVE5514907BEE0486-1EGAR00001135446
BEEHIVE5514907BEE0486-1EGAR00001143134
BEEHIVE5514906BEE0485-1EGAR00001135445
BEEHIVE5514906BEE0485-1EGAR00001143133
BEEHIVE5514905BEE0484-1EGAR00001135444
BEEHIVE5514905BEE0484-1EGAR00001143132
BEEHIVE5514904BEE0483-1EGAR00001143131
BEEHIVE5514904BEE0483-1EGAR00001135443
BEEHIVE5514903BEE0482-1EGAR00001135442
BEEHIVE5514903BEE0482-1EGAR00001143130
BEEHIVE5514902BEE0481-1EGAR00001143129
BEEHIVE5514902BEE0481-1EGAR00001135441
BEEHIVE5514901BEE0480-1EGAR00001143128
BEEHIVE5514901BEE0480-1EGAR00001135440
BEEHIVE5514900BEE0479-1EGAR00001143127
BEEHIVE5514900BEE0479-1EGAR00001135439
BEEHIVE5514899BEE0478-1EGAR00001143126
BEEHIVE5514899BEE0478-1EGAR00001135438
BEEHIVE5514898BEE0477-1EGAR00001135437
BEEHIVE5514898BEE0477-1EGAR00001143125

HIV genome sequencing

Sample

Strain

Run Accession

3761_HIV_T146UnknownERR261718
3760_HIV_T146UnknownERR261717
3759_HIV_T146UnknownERR261716
3758_HIV_T146UnknownERR261715
3757_HIV_T146UnknownERR261714
3756_HIV_T146UnknownERR261713
3755_HIV_T146UnknownERR261712
3754_HIV_T146UnknownERR261711
3753_HIV_T146UnknownERR261710
3752_HIV_T146UnknownERR261709
3751_HIV_T146UnknownERR261708
3750_HIV_T146UnknownERR261707
479STDY55397914318_HIV_T146ERR338746
479STDY55397904317_HIV_T146ERR338745
479STDY55397894316_HIV_T146ERR338744
479STDY55397884315_HIV_T146ERR338743
479STDY55397874314_HIV_T146ERR338742
479STDY55397864313_HIV_T146ERR338741
479STDY55397854312_HIV_T146ERR338740
479STDY55397824309_HIV_T146ERR338739
479STDY55397814308_HIV_T146ERR338738
479STDY55397804307_HIV_T146ERR338737
479STDY55397794306_HIV_T146ERR338736
479STDY55397784305_HIV_T146ERR338735
479STDY55397774304_HIV_T146ERR338734
479STDY55397744301_HIV_T146ERR338733
479STDY55397734300_HIV_T146ERR338732
479STDY55398094367_HIV_T146ERR338731
479STDY55398084366_HIV_T146ERR338730
479STDY55398074365_HIV_T146ERR338729
479STDY55398064364_HIV_T146ERR338728
479STDY55398054332_HIV_T146ERR338727
479STDY55398044331_HIV_T146ERR338726
479STDY55398014328_HIV_T146ERR338725
479STDY55398004327_HIV_T146ERR338724
479STDY55397994326_HIV_T146ERR338723
479STDY55397984325_HIV_T146ERR338722
479STDY55397974324_HIV_T146ERR338721
479STDY55397964323_HIV_T146ERR338720
479STDY55397934320_HIV_T146ERR338719
479STDY55397924319_HIV_T146ERR338718
479STDY55398104368_HIV_T146ERR346905
479STDY55398034330_HIV_T146ERR346904
479STDY55398024329_HIV_T146ERR346903
479STDY55397954322_HIV_T146ERR346902
479STDY55397944321_HIV_T146ERR346901
479STDY55397844311_HIV_T146ERR346900
479STDY55397834310_HIV_T146ERR346899
479STDY55397764303_HIV_T146ERR346898
479STDY55397754302_HIV_T146ERR346897
479STDY55799022375_HIV_T146ERR381524
479STDY57134575629_HIV_T146ERR490393
479STDY57134565628_HIV_T146ERR490392
479STDY57134555627_HIV_T146ERR490391
479STDY57134545626_HIV_T146ERR490390
479STDY57134535625_HIV_T146ERR490389
479STDY57134525624_HIV_T146ERR490388
479STDY57134515623_HIV_T146ERR490387
479STDY57134505622_HIV_T146ERR490386
479STDY57134495621_HIV_T146ERR490385
479STDY57134485620_HIV_T146ERR490384
479STDY57134475619_HIV_T146ERR490383
479STDY57134465618_HIV_T146ERR490382
479STDY57134455617_HIV_T146ERR490381
479STDY57134445616_HIV_T146ERR490380
479STDY57134435615_HIV_T146ERR490379
479STDY57134425614_HIV_T146ERR490378
479STDY57134415613_HIV_T146ERR490377
479STDY57134405612_HIV_T146ERR490376
479STDY57134395611_HIV_T146ERR490375
479STDY57134385610_HIV_T146ERR490374
479STDY57134645636_HIV_T146ERR490400
479STDY57134635635_HIV_T146ERR490399
479STDY57134625634_HIV_T146ERR490398
479STDY57134615633_HIV_T146ERR490397
479STDY57134605632_HIV_T146ERR490396
479STDY57134595631_HIV_T146ERR490395
479STDY57134585630_HIV_T146ERR490394

Data Use Statement

This sequencing centre plans on publishing the completed and annotated sequences in a peer-reviewed journal as soon as possible. Permission of the principal investigator should be obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or genome scale. See our data sharing policy.

Sequencing enquiries

Please address all sequencing enquiries to: pathinfo@sanger.ac.uk

* quick link - http://q.sanger.ac.uk/w3y4rfw0