Learn more about our New BaseScopeTM assay

HIV/SIV Research

Detection of SIV using non-isotopic ISH compared to the RNAscope ISH (red). Data courtesy of Dr. Jacob Estes of NCI

Detection of SIV using non-isotopic ISH compared to the RNAscope ISH (red). Data courtesy of Dr. Jacob Estes of NCI

Detection of HIV RNA in human CD3+ T cells in the spleen of humanized BLT mice using RNAscope 2.0 HD Reagent Kit-RED. RNAscope ISH was followed by colorimetric immunohistochemistry for human T cells using mAb to human CD3, and nuclei were counterstained

Detection of HIV RNA in human CD3+ T cells in the spleen of humanized BLT mice using RNAscope 2.0 HD Reagent Kit-RED. RNAscope ISH was followed by colorimetric immunohistochemistry for human T cells using mAb to human CD3, and nuclei were counterstained

HIV in human lung tissue

HIV in human lung tissue

Despite the remarkable success of antiretroviral therapy (ART), the persistence of HIV reservoirs is a major barrier to overcome in finding a lasting cure. In order to completely eradicate HIV and advance therapeutic interventions, it is important to elucidate the biological nature of viral latency as well as productively infected cells in tissues including the gastrointestinal tract and those of the lymphatic system. RNAscope®, a highly specific and sensitive in-situ hybridization technology, employs a powerful technique to study HIV and SIV in cellular and tissue environments.

Why use RNAscope® Assay for HIV and SIV research?

  • Localize specific cell types and tissues infected with HIV/SIV – ideal for identifying and measuring persistent reservoirs with single-cell resolution in full morphological context.

  • Detect HIV/SIV RNA sequences despite low or undetectable plasma viral loads with specificity – with single RNA molecule detection technology, identify individual virus particles and infected cells.

  • Differential detection of viral RNA and proviral DNA – RNAscope® probes can be designed to target the sense or antisense sequences to detect the three different configurations of HIV/SIV during the replication cycles:

    • viral RNA in a virus particle;

    • viral genomic RNA or mRNA in an infected cell;

    • proviral DNA integrated in the nucleus of an infected cell.

 

Read Science 's news article 'Molecular microscope' finds hidden AIDS virus in the body" about Jake Estes of the Frederick National Laboratory of the National Cancer Institute and the application of RNAscope® technology in HIV/SIV research.  Dr. Estes and collaborators recently authored a publication Defining HIV and SIV Reservoirs in Lymphoid Tissues.  The team of researchers outline methodology to visualize viral RNA and viral DNA simultaneously in HIV-1/SIV.  Read more

"The identification and anatomic location of HIV-infected cells and the effects of tissu e environment on virus replication and viral gene expression are all critical for evaluating the pathogenesis of HIV infection and for developing cure strategies to eliminate HIV reservoirs. RNAscope in situ hybridization (ISH) has enabled us to visualize and quantify HIV RNA with single-copy resolution. For work supported by a Federal Contract with NIAID, NIH, we are using this state-of-the-art ISH technology in combination with immunohistochemistry to charactoerize the tissue and cellular compartments where the virus resides in HIV-infected humanized mice."

UCSF School of Medicine.  Recent publications citing RNAscope® assay:J Neurovirol. 2015 Nov 16. PMID: 26572785.

RNAscope® Catalog Probes Targeting HIV: 

(Listed below are probes for manual RNAscope assay. Corresponding probes for automated assays are also available. )

Target species & region

Cat. No & Probe Description

HIV1

Targeting Env, Gag, Pol genes

450141       Probe-V-HIV1-env

450151       Probe-V-HIV1-env-sense

311921       Probe-V-HIV1 (Gag)

446211-C2 Probe-V-HIV1-Gag-C2

317691       Probe-V-HIV1-gagpol

317701       Probe-V-HIV1-gagpol-sense

317701-C2 Probe-V-HIV1-gagpol-sense-C2

445651       Probe-V-HIV1-gagpol-sense-scrambled

445651-C2 Probe-V-HIV1-gagpol-sense-scrambled-C2

HIV1,

Excluding Gag and Pol genes

317711       Probe-V-HIV1-nongagpol

317711-C2 Probe-V-HIV1-nongagpol-C2

453631       Probe-V-HIV1-nongagpol-scrambled

317721       Probe-V-HIV1-nongagpol-sense

317721-C3 Probe-V-HIV1-nongagpol-sense-C3

445661       Probe-V-HIV1-nongagpol-sense-scrambled

HIV1,

Subtype A

416101       Probe-V-HIV1-CladeA

426341       Probe-V-HIV1-CladeA-sense

HIV1,

Subtype B

416111       Probe-V-HIV1-CladeB

416111-C2 Probe-V-HIV1-CladeB-C2

444051       Probe-V-HIV1-CladeB-gag-pol-sense

447711       Probe-V-HIV1-CladeB-scrambled

425531       Probe-V-HIV1-CladeB-sense

425531-C2 Probe-V-HIV1-CladeB-sense-C2

425531-C3 Probe-V-HIV1-CladeB-sense-C3

444061-C2 Probe-V-HIV1-CladeB-vif-vpr-tat-rev-vpu-env-nef-tar-C2

HIV1,

Subtype C

429841       Probe-V-HIV1-CladeC

444021       Probe-V-HIV1-CladeC-gag-pol-sense

430171       Probe-V-HIV1-CladeC-sense

444041-C2 Probe-V-HIV1-CladeC-vif-vpr-rev-vpu-env-nef-tar-C2

HIV1,

Subtype D

416121       Probe-V-HIV1-CladeD

426351       Probe-V-HIV1-CladeD-sense

HIV1,

Subtype AE

446551       Probe-V-HIV-CladeAE

444011       Probe-V-HIV1-CladeAE-gag-pol-sense

444031-C2  Probe-V-HIV1-CladeAE-vif-vpr-tat-rev-vpu-env-nef-tar-C2

HIV2

446221-C3  Probe-V-HIV2-gag-C3

 

RNAscope® Catalog Probes Targeting SIV: 

(Listed below are probes for manual RNAscope assay. Corresponding probes for automated assays are also available. )

Target SIV strain

Cat. No & Probe Description

SIV-Mac329

(rhesus monkey, Macaca mulatta)

312811        Probe-SIVmac239

312811-C2  Probe-SIVmac239-C2

314071        Probe-SIVmac239-sense

314071-C2  Probe-SIVmac239-sense-C2

314451        Probe-SIVmac239-gag

445431        Probe-V-SIVmac239-rev-env

445441        Probe-V-SIVmac239-vif-vpr-tat

416131        Probe-V-SIVmac239-vif-env-nef-tar

416131-C2  Probe-V-SIVmac239-vif-env-nef-tar-C2

416141        Probe-V-SIVmac239-gag-pol-sense

416141-C2  Probe-V-SIVmac239-gag-pol-sense-C2

459071-C3  Probe-V-SIVmac239-vif-env-nef-tar-sense-C3

SIV-amg

(african green monkey, Cercopithecus aethiops)

431811       Probe-V-SIV-gag

431821       Probe-V-SIV-pol

431831       Probe-V-SIV-rev-env

431841       Probe-V-SIV-vif-vpr-tat

432081       Probe-V-SIV

SIV-sm sooty mangabey

(sooty mangabey, Cercocebus atys)

415351       Probe-V-SIVsmm

To target other HIV/SIV strains or regions, ACD can design and manufacture MADE-TO-ORDER Probes  in just 2 weeks. 

Related Publications

Recent publications where RNAscope® assay was used to detect HIV or SIV.

TitleAuthorsJournalPubMed IDYear
The meningeal lymphatic system: a route for HIV brain migration?Lamers SL, Rose R, Ndhlovu LC, Nolan DJ, Salemi M, Maidji E, Stoddart CA, McGrath MS.J Neurovirol. 2015 Nov 16.PMID: 265727852015
CD4 depletion in SIV-infected macaques results in macrophage and microglia infection with rapid turnover of infected cells.Micci L, Alvarez X, Iriele RI, Ortiz AM, Ryan ES, McGary CS, Deleage C, McAtee BB, He T, Apetrei C, Easley K, Pahwa S, Collman RG, Derdeyn CA, Davenport MP, Estes JD, Silvestri G, Lackner AA, Paiardini M.PLoS Pathog. 2014 Oct 30;10(10):e1004467.PMID: 25356757 | doi: 10.1371/journal.ppat.1004467.2014
B cell follicle sanctuary permits persistent productive simian immunodeficiency virus infection in elite controllers.Fukazawa Y, Lum R, Okoye AA, Park H, Matsuda K, Bae JY, Hagen SI, Shoemaker R, Deleage C, Lucero C, Morcock D, Swanson T, Legasse AW, Axthelm MK, Hesselgesser J, Geleziunas R, Hirsch VM, Edlefsen PT, Piatak M Jr, Estes JD, Lifson JD, Picker LJ.Nat Med. 2015 Jan 19.PMID: 25599132 | doi: 10.1038/nm.3781.2015
Effect of Suberoylanilide Hydroxamic Acid (SAHA) Administration on the Residual Virus Pool in a Model of Combination Antiretroviral Therapy-Mediated Suppression in SIVmac239-Infected Indian Rhesus Macaques.Del Prete GQ, Shoemaker R, Oswald K, Lara A, Trubey CM, Fast R, Schneider DK, Kiser R, Coalter V, Wiles A, Wiles R, Freemire B, Keele BF, Estes JD, Quiñones OA, Smedley J, Macallister R, Sanchez RI, Wai JS, Tan CM, Alvord WG, Hazuda DJ, Piatak M Jr, Lifson JD.Antimicrob Agents Chemother. 2014 Nov;58(11):6790-806.PMID: 25182644 |doi: 10.1128/AAC.03746-14.2014
Tracking the Luminal Exposure and Lymphatic Drainage Pathways of Intravaginal and Intrarectal Inocula Used in Nonhuman Primate Models of HIV Transmission.Smedley J, Turkbey B, Bernardo ML, Del Prete GQ, Estes JD, Griffiths GL, Kobayashi H, Choyke PL, Lifson JD, Keele BF.PLoS One. 2014 Mar 25;9(3):e92830.PMID: 24667371 | doi: 10.1371/journal.pone.0092830.2014
Administration of Panobinostat Is Associated with Increased IL-17A mRNA in the Intestinal Epithelium of HIV-1 PatientsChristensen AB, Dige A, Vad-Nielsen J, Brinkmann CR, Bendix M, Østergaard L, Tolstrup M, Søgaard OS, Rasmussen TA, Nyengaard JR, Agnholt J, Denton PW.Mediators of Inflammation (2015)http://dx.doi.org/10.1155/2015/1206052015
X
Contact Us

Complete one of the two forms below and we will get back to you.

Advanced Cell Diagnostics

Our new headquarters office starting May 2016:

7707 Gateway Blvd.  
Newark, CA 94560
Toll Free: 1 (877) 576-3636
Phone: (510) 576-8800
Fax: (510) 576-8798

 

Advanced Cell Diagnostics , S.r.l.

Via Calabria15
20090 Segrate (Milano) - Italy

Phone: +39.02.95360323
Fax: +39.02.95360992
For European orders: order_europe@acdbio.com

Advanced Cell Diagnostics China

Building 15, No. 26 Xihuan South Road
Beijing Economic-Technological Development Area
Beijing, China, Zip code: 100176

400-966-1796
info_china@acdbio.com
For general information: Leon Li lli@acdbio.com
Web: www.acdbio.com.cn

For general information: info@acdbio.com
For place an order: order@acdbio.com
For product support: support@acdbio.com
For career opportunities: hr@acdbio.com