Rotavirus RNA PCR - stool specimen

Collect

Stool in a sterile, leak-proof container

Volume Required

2 to 4 ml of liquid stool; 2 to 4 grams of formed stool

Minimum Required

2 ml of liquid stool; 2 grams of formed stool

Transport

Keep specimen at 4C

Stability

Labile

Processing

The specimen of choice is stool. Although acceptable, rectal swabs are inferior to stool specimens for the detection of viruses and are discouraged. If it is necessary to collect a rectal swab, a sufficient quantity of fecal material (at least a pea-sized amount) should
be obtained. If fecal material is not clearly visible on the swab, the specimen is most likely inadequate. Rectal swabs should be immediately placed in viral transport medium. Specimens should be transported to the laboratory as quickly as possible after collection. When immediate transport is not possible, refrigerate the specimens or keep them on wet ice. For delays of more than 24-48 hours (e.g., when shipping specimens from an outside facility), specimens should be processed as needed and rapidly frozen to -70C and then transported to the laboratory on dry ice.

Unacceptable conditions

Specimens for molecular testing should not be stored at room temperature or frozen at -20C. This is critical to ensure the stability and amplification of nucleic acids, particularly for the detection of RNA viruses since RNA is unstable and easily degraded by RNAses from the surrounding environment.

Rectal swab specimens not received in viral transport medium or received in bacteriological transport medium are discouraged. DO NOT USE CALCIUM ALGINATE OR WOODEN SHAFT SWABS FOR COLLECTION OF SPECIMENS; ONLY USE DACRON OR RAYON TIPPED SWABS ON PLASTIC OR METAL SHAFTS.

Days Performed

Daily, Monday thru Friday

Reported

1-3 days

CPT

87798

Methodology

Amplification and detection of rotavirus RNA using real-time TaqMan PCR and nucleic acid primer/probe pairs specific for a conserved region of the inner capsid protein VP6 gene. This test is performed pursuant to an agreement with Roche Molecular Systems, Inc.

Disease Information

Clinical Features:

Gastroenteritis is one of the most common illnesses affecting infants, children, and adults worldwide. It can be caused by a number of different pathogens, including viruses, bacteria, fungi, and parasites and can be difficult to distinguish on the basis of clinical criteria alone. Severe disease leading to hospitalization, increased morbidity, and even death is observed among infants, children, the elderly, and the immunocompromised. Acute infectious gastroenteritis is characterized by a variety of symptoms and signs. Affected individuals typically have diarrhea, vomiting, fever, abdominal cramps, dehydration, irritability, and lethargy. Headache, anorexia, malaise, myalgia, and nausea are often observed in adults but can be difficult to assess in children. The presentation can vary widely from only upper gastrointestinal symptoms of vomiting to acute diarrhea without vomiting. Symptoms can appear alone or together and can mimic illness caused by drugs, toxins, or other conditions. Viruses cause most of the acute infectious gastroenteritis; bacteria and protozoa are the cause in 20 to 25%; <50% have an established etiology. Viral gastroenteritis is caused by a variety of viruses, the most important of which are rotavirus, norovirus genogroups I & II, the enteric adenovirus types 40 & 41, astrovirus and sapovirus. These viruses present with a similar disease; onset is sudden (1 to 2 d after infection) and the illness is normally of short duration (<7 days; may last 1 to 10 days, depending on the virus). The stools are watery with no mucous or blood; fecal leukocytes are absent or minimal in number. Viral gastroenteritis is often called “stomach flu”; it is self-limited in healthy, well-nourished persons and asymptomatic infections or mild disease are very common. Serious disease can occur in those unable to rehydrate and chronic diarrhea, increased mortality, and prolonged fecal shedding of infectious virus is often seen in immunocompromised hosts. Viral gastroenteritis is highly contagious; an infective dose in a child can be as few as 10 viral particles. Spread is by the fecal-oral route through close contact with infected persons. Individuals can become infected through intermediary contaminated fomites (e.g. shared eating utensils, surfaces, toys in playrooms, door knobs, elevator buttons, bed rails, toilet seats) and by eating or drinking contaminated foods or beverages. Respiratory secretions are thought to possibly transmit these viruses as well. Nosocomial (hospital-acquired) spread is significant for rotavirus, but has also been reported for the enteric adenoviruses, astrovirus, and norovirus. Because of the physical hardiness of GI viruses, they are efficiently transmitted from an infected person to others. GI viruses are stable over wide pH and temperature ranges and even after drying, heating, or freezing and are stable on human hands and objects for extended times. High virus concentrations exist in stools, and these viral agents are often resistant to inactivation by various standard cleaning solutions; they can be inactivated by antiseptic agents that contain high concentrations (>40%) of alcohols (e.g., Purell and Lysol) and by household bleach. GI viruses most often have a seasonal peak in the winter months, but infections do occur year-round.

Rotavirus belongs to the Family Reoviridae and is a non-enveloped virus possessing a double-stranded, segmented RNA genome composed of 11 segments. Rotavirus is the leading cause of severe, dehydrating diarrhea in infants and young children worldwide. Globally, the CDC estimates that it causes more than a half a million deaths each year in children younger than 5 years of age. Prior to the introduction of rotavirus vaccine to the U.S. in 2006, rotavirus infections resulted in more than 400,000 doctor visits; 200,000 emergency room visits; 55,000 to 70,000 hospitalizations; and 20 to 60 deaths each year in young children.

Utility:

Because the clinical features of viral gastroenteritis do not differ from those of gastroenteritis caused by other pathogens, laboratory testing is required for reliable diagnosis. Unfortunately, there are many issues involved in the laboratory diagnosis of viral gastroenteritis and detection of GI viruses can be very difficult. As a result, much of viral GI disease goes unrecognized. GI viruses do not grow well, if at all, in standard cell culture systems used in clinical laboratories and there is a definite lack of available reagents and assays for clinical use. Commercial rapid antigen detection tests are available for rotavirus and, to a lesser extent, for adenovirus 40/41 and norovirus; they offer speed in the diagnosis of viral GI disease but are not completely sensitive. The polymerase chain reaction (PCR) offers great promise for the diagnosis of viral gastroenteritis and has emerged as the most sensitive and specific method for the detection of viral causes of diarrhea. Why test for GI viruses? There are many important reasons---(a) Infection Control-to prevent or reduce community and hospital spread, (b) Individual Patient Management-provide a specific diagnosis and earlier informed decision making for better care, help manage special populations (e.g., transplant, cancer, HIV, those in ICUs, patients of a certain age or with underlying medical conditions, help guide treatment decisions, help reduce or stop unnecessary antimicrobials, laboratory tests, and hospital procedures, help reduce the morbidity and increased hospital stay and costs associated with not having a defined diagnosis, and for education and clinical awareness, and (c) Surveillance-rapid outbreak identification at local, regional, national, and global levels.

Interpretation

If positive, results are reported as rotavirus RNA detected

Reference Values

Negative or no rotavirus RNA detected