Watch Presentation on RNAscope for Viral Pathogenesis Research

Viral Pathogen Detection & Visualization

HCV-uninfected (left) or HCV-infected (right) HuH-7 cells were hybridized with probes targeting HCV mRNA (green). Cells were costained with 18S rRNA target probes (red) as an internal control for assay success. Nuclei were counterstained with DAPI (blue).

HCV-uninfected (left) or HCV-infected (right) HuH-7 cells were hybridized with probes targeting HCV mRNA (green). Cells were costained with 18S rRNA target probes (red) as an internal control for assay success. Nuclei were counterstained with DAPI (blue).

Direct detection of viral RNA in human or other animal cells by RNA in situ hybridization (ISH) is a powerful tool to establish the etiology and pathogenesis of viral diseases. Nucleic acid-based molecular detection methods have revolutionized viral detection, offering several essential advantages such as sensitivity, specificity and speed.  Beyond those stated advantages, RNAscope  ISH uniquely offers molecular detection coupled with morphological context enabling visualization of the virus in different infected tissues and cell types. 

Why use RNAscope™ assay for viral pathogen research?

Sensitivity—with single RNA molecule detection technology, RNAscope ISH routinely identify individual viral particles in infected cells despite low or undetectable viral loads. Its high sensitivity level enables detection even in early stages of infection.

Specificity—proprietary probe design strategy enables accurate detection among highly related viral species/strains, providing accurate detection even in the presence of contaminants or similar/related viruses.

Speed—single-day workflow coupled with rapid 2 weeks new probe design and manufacture process makes RNAscope ISH a responsive solution for detection of emerging or exotic viruses.

Localization—providing both accurate molecular detection and visualization of infected cell types and tissues enables elucidation of viral transmission, pathogen-host interactions, localization of hidden reservoirs, etc.

Coinfection detection—RNAscope  duplex and multiplex assays offer the possibility of detecting multiple viruses or co-infection.

Differential detection—flexible probe design targeting the sense or anti-sense strand enables detection and differentiation of virus during latent or active stages

  •  e.g. Retroviruses—RNAscope probes can be designed for detection of viral RNA in a virus particle; viral genomic RNA or mRNA in an infected cell; pro-viral DNA integrated in the nucleus of an infected cell.
  •  e.g.  (+)ssRNA virus—RNAscope probes designed to target the sense strand detects viral genomic RNA and those designed to target the antisense strand detects complementary RNA (template of transcription/replication) 

RNAscope ISH and other viral detection methods

Real-time PCR assay is a sensitive, rapid and cost effective viral detection method.  However, this grind and bind method does not preserve morphological context and provides expression level averaged across the cell population and not at the single cell level. Researchers use PCR methods to detect and quantify viral presence and apply RNAscope ISH to compliment PCR data with single-cell expression level and localization.

NGS is a powerful a priori method especially valued for viral discovery and detection.  In the case of viral discovery, researchers use this new sequence to obtain RNAscope probes for detection and visualization of the virus within is infected environment. In the case of viral detection, NGS, a grind and bind method, does not preserve morphological context.

IHC/ Immuno-based techniques rely on detection of host antibodies against the virus or capturing viral components using antibodies raised against them. Although these indirect viral detection techniques offer morphological context, they are are becoming less routine due to lack of sensitivity and cost of custom antibody production. Compared to IHC, RNAscope ISH is preferred due to its unrivaled sensitivity and specificity along with its probe design accommodating detection of virtually any gene in any tissue of any species. 

Additional information is available on RNAscope applications in HIV/SIV and Zika viral research. 

RNAscope Catalog Probes are available for over 100 different viral species and ever growing. Click on species name to see corresponding probes.

Adeno-associated virus

Alpaca Polyomavirus

Andes virus

Avian infectious bronchitis virus

Bat hepadnavirus

Bat hepatovirus

Bovine astrovirus

Bovine papillomavirus

Bovine parvovirus

Canine bocavirus

Canine herpesvirus

Canine papillomavirus

Canine parvovirus

Cercopithecine herpesvirus

Chikungunya virus


Citrus tristeza virus

COVID-19 coronavirus

Cynomolgus macaque cytomegalovirus

Dengue virus

Eastern equine encephalitis virus


Equid herpesvirus

Equine arteritis virus

Felid herpesvirus

Feline immunodeficiency virus

Feline infectious peritonitis virus

Feline papillomavirus

Frog virus

Hedgehog hepatovirus

Hendra virus


Hepatitis B virus

Hepatitis C virus

Hepatitis D Virus

Hepatitis E Virus

Hepatitis GB Virus

Human betacoronavirus

Human bocavirus

Human coronavirus

Human coxsackievirus

Human endogenous retrovirus

Human herpesvirus

Human immunodeficiency virus 1

Human papillomavirus

Human parechovirus

Human parvovirus

Human rhinovirus

Human T-lymphotropic virus 1

Influenza virus

Japanese encephalitis virus


Langat virus

Lassa virus

Lymphocytic choriomeningitis virus

Macacine herpesvirus

Marburg virus

Measles virus

Merkel cell polyomavirus

Middle East respiratory syndrome coronavirus

Mumps virus

Murine herpesvirus

Mus musculus papillomavirus type

Newcastle disease virus

Nipah virus 


Ovine herpesvirus

Ovine herpesvirus


Parvo like virus

Phocoenid herpesvirus

Porcine astrovirus

Porcine parainfluenza virus

Powassan virus

Rabies virus

Raccoon polyomavirus

Respiratory Syncytial Virus

Retroperitoneal fibromatosis-associated herpesvirus

Rhesus cytomegalovirus

Rodent hepacivirus

Rodent hepatovirus


Rubella virus

SARS coronavirus

Self-complementary adeno-associated virus

Seneca valley virus

Severe fever with thrombocytopenia syndrome virus

Shrew hepadnavirus

Shrew hepatovirus

Simian hemorrhagic fever virus

Simian immunodeficiency virus

Simian parvovirus

Simian virus 40

Sin Nombre hantavirus

Theiler's disease-associated virus

Vaccinia virus

Venezuelan equine encephalitis virus

Vesicular stomatitis Indiana virus

Yellow fever virus

Zaire Ebola virus

Zika virus



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