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

BEEHIVE55149453860_HIV_T146EGAR00001135484
BEEHIVE55149443859_HIV_T146EGAR00001135483
BEEHIVE55149443859_HIV_T146EGAR00001143171
BEEHIVE55149433858_HIV_T146EGAR00001135482
BEEHIVE55149433858_HIV_T146EGAR00001143170
BEEHIVE55149423857_HIV_T146EGAR00001135481
BEEHIVE55149423857_HIV_T146EGAR00001143169
BEEHIVE55149413856_HIV_T146EGAR00001135480
BEEHIVE55149413856_HIV_T146EGAR00001143168
BEEHIVE55149403855_HIV_T146EGAR00001135479
BEEHIVE55149403855_HIV_T146EGAR00001143167
BEEHIVE55149393854_HIV_T146EGAR00001135478
BEEHIVE55149393854_HIV_T146EGAR00001143166
BEEHIVE55149383853_HIV_T146EGAR00001135477
BEEHIVE55149383853_HIV_T146EGAR00001143165
BEEHIVE55149373852_HIV_T146EGAR00001135476
BEEHIVE55149373852_HIV_T146EGAR00001143164
BEEHIVE55149363851_HIV_T146EGAR00001135475
BEEHIVE55149363851_HIV_T146EGAR00001143163
BEEHIVE55149353850_HIV_T146EGAR00001135474
BEEHIVE55149353850_HIV_T146EGAR00001143162
BEEHIVE55149343849_HIV_T146EGAR00001135473
BEEHIVE55149343849_HIV_T146EGAR00001143161
BEEHIVE55149333848_HIV_T146EGAR00001135472
BEEHIVE55149333848_HIV_T146EGAR00001143160
BEEHIVE55149323847_HIV_T146EGAR00001135471
BEEHIVE55149323847_HIV_T146EGAR00001143159
BEEHIVE55149313846_HIV_T146EGAR00001135470
BEEHIVE55149313846_HIV_T146EGAR00001143158
BEEHIVE55149303845_HIV_T146EGAR00001135469
BEEHIVE55149303845_HIV_T146EGAR00001143157
BEEHIVE55149293844_HIV_T146EGAR00001135468
BEEHIVE55149293844_HIV_T146EGAR00001143156
BEEHIVE55149283843_HIV_T146EGAR00001135467
BEEHIVE55149283843_HIV_T146EGAR00001143155
BEEHIVE55149273842_HIV_T146EGAR00001135466
BEEHIVE55149273842_HIV_T146EGAR00001143154
BEEHIVE55149263841_HIV_T146EGAR00001135465
BEEHIVE55149263841_HIV_T146EGAR00001143153
BEEHIVE55149253840_HIV_T146EGAR00001135464
BEEHIVE55149253840_HIV_T146EGAR00001143152
BEEHIVE55149243839_HIV_T146EGAR00001135463
BEEHIVE55149243839_HIV_T146EGAR00001143151
BEEHIVE55149233838_HIV_T146EGAR00001135462
BEEHIVE55149233838_HIV_T146EGAR00001143150
BEEHIVE55149223837_HIV_T146EGAR00001135461
BEEHIVE55149223837_HIV_T146EGAR00001143149
BEEHIVE55149213836_HIV_T146EGAR00001135460
BEEHIVE55149213836_HIV_T146EGAR00001143148
BEEHIVE55149203835_HIV_T146EGAR00001135459
BEEHIVE55149203835_HIV_T146EGAR00001143147
BEEHIVE55149193834_HIV_T146EGAR00001135458
BEEHIVE55149193834_HIV_T146EGAR00001143146
BEEHIVE55149183833_HIV_T146EGAR00001135457
BEEHIVE55149183833_HIV_T146EGAR00001143145
BEEHIVE55149173832_HIV_T146EGAR00001135456
BEEHIVE55149173832_HIV_T146EGAR00001143144
BEEHIVE55149163831_HIV_T146EGAR00001135455
BEEHIVE55149163831_HIV_T146EGAR00001143143
BEEHIVE55149153830_HIV_T146EGAR00001135454
BEEHIVE55149153830_HIV_T146EGAR00001143142
BEEHIVE55149143829_HIV_T146EGAR00001135453
BEEHIVE55149143829_HIV_T146EGAR00001143141
BEEHIVE55149133828_HIV_T146EGAR00001135452
BEEHIVE55149133828_HIV_T146EGAR00001143140
BEEHIVE55149123827_HIV_T146EGAR00001135451
BEEHIVE55149123827_HIV_T146EGAR00001143139
BEEHIVE55149113826_HIV_T146EGAR00001135450
BEEHIVE55149113826_HIV_T146EGAR00001143138
BEEHIVE55149103825_HIV_T146EGAR00001135449
BEEHIVE55149103825_HIV_T146EGAR00001143137
BEEHIVE55149093824_HIV_T146EGAR00001135448
BEEHIVE55149093824_HIV_T146EGAR00001143136
BEEHIVE55149083823_HIV_T146EGAR00001135447
BEEHIVE55149083823_HIV_T146EGAR00001143135
BEEHIVE55149073822_HIV_T146EGAR00001135446
BEEHIVE55149073822_HIV_T146EGAR00001143134
BEEHIVE55149063821_HIV_T146EGAR00001135445
BEEHIVE55149063821_HIV_T146EGAR00001143133
BEEHIVE55149053820_HIV_T146EGAR00001135444
BEEHIVE55149053820_HIV_T146EGAR00001143132
BEEHIVE55149043819_HIV_T146EGAR00001135443
BEEHIVE55149043819_HIV_T146EGAR00001143131
BEEHIVE55149033818_HIV_T146EGAR00001135442
BEEHIVE55149033818_HIV_T146EGAR00001143130
BEEHIVE55149023817_HIV_T146EGAR00001135441
BEEHIVE55149023817_HIV_T146EGAR00001143129
BEEHIVE55149013816_HIV_T146EGAR00001135440
BEEHIVE55149013816_HIV_T146EGAR00001143128
BEEHIVE55149003815_HIV_T146EGAR00001135439
BEEHIVE55149003815_HIV_T146EGAR00001143127
BEEHIVE55148993814_HIV_T146EGAR00001135438
BEEHIVE55148993814_HIV_T146EGAR00001143126
BEEHIVE55148983813_HIV_T146EGAR00001135437
BEEHIVE55148983813_HIV_T146EGAR00001143125

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

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/e6k4v2ic