New web-based resources addressing the 2009 H1N1 virus pandemic are available:
PubMed added useful links to its homepage, including one to publications recently added and another to GeneBank's H1N1 sequences. An FDA page devoted to testing reiterates that "no influenza tests are sufficiently sensitive to rule out an influenza infection, and clinicians must consider clinical and epidemiological criteria along with laboratory testing results."
The CDC's page devoted to clinical laboratory issues, lists links to other pages in the CDC site as well as a link to the Association of Public Health Laboratories' homepage, from where you can access their H1N1 page. Three links to pages in the WHO site ("Protocol for Antiviral Susceptibility Testing by PyrosequencingExternal Web Site Policy", "Sequencing Primers and Protocol" and "CDC Protocol of Realtime RTPCR for Swine Influenza A(H1N1)"), refer to sequencing and molecular testing.
The U.S. Government Pandemic Flu site now addresses the 2009 H1N1 virus.
Showing posts with label Tests. Show all posts
Showing posts with label Tests. Show all posts
Tuesday, May 5, 2009
Sunday, May 3, 2009
Rapid influenza antigen testing recommendations
On Friday, the CDC posted recommendations for the use of rapid influenza testing in the assessment of patients suspected of having the SOIV H1N1 virus.
The Festschrift Symposium in Honor of Peter Jatlow, MD takes place in New Haven, CT. today. Dr. Jatlow, former Chairman of the Department of Laboratory Medicine at YaleUniversity, Director of Laboratories at Yale-New Haven Hospital, and an authority on the clinical chemistry of addiction, presided over the training of numerous promotions of clinical pathologists, many of whom will be attending.
The Festschrift Symposium in Honor of Peter Jatlow, MD takes place in New Haven, CT. today. Dr. Jatlow, former Chairman of the Department of Laboratory Medicine at YaleUniversity, Director of Laboratories at Yale-New Haven Hospital, and an authority on the clinical chemistry of addiction, presided over the training of numerous promotions of clinical pathologists, many of whom will be attending.
Guidance on Specimen Collection and Rapid Testing
Roberta Carey, Acting Director of the Division of Laboratory Systems at the CDC made available an interim draft list of answers to Frequently Asked Questions from laboratories on May 1st. Since I could not find a link to this letter, I include a copy below:
Frequently Asked Questions on Swine Flu (H1N1) from the Laboratories
Frequently Asked Questions on Swine Flu (H1N1) from the Laboratories
1. What specimens are acceptable for the recovery of swine flu?
The preferred respiratory specimens include: nasopharyngeal swab/aspirate or nasal wash/aspirate. If these specimens cannot be collected, a combined nasal swab with an oropharyngeal swab is acceptable. For patients who are intubated, an endotracheal aspirate should also be collected. Specimens should be placed into sterile viral transport media (VTM) and immediately placed on ice or cold packs or at 4°C (refrigerator) for transport to the laboratory.
2. If swabs are used to collect a specimen, which ones are acceptable?
There are a variety of swabs with a synthetic tip shown to have superior recovery of viruses, such as the flocked swabs. Avoid cotton tipped swabs, calcium-alginate swabs and those with a wooden shaft, which would inhibit the recovery of the virus, and may not be approved for use with the rapid testing kits.
3. If I receive a swab for rapid testing, I have nothing left to send for confirmation. What should I do?
You may ask your clinicians to collect two swabs. If your rapid test is positive for influenza A, then send the second swab to the public health lab for testing. Ideally the second swab should be immersed in viral transport media during transport. If only one swab is received, you may have leftover diluent where the cells from the swab were extracted that could be suitable for further testing. It is unknown at this time if these diluents or saline are compatible with the confirmatory tests.
4. I don’t have access to dry ice, how can I ship specimens to my public health lab?
It is acceptable to place the specimens in appropriately sealed shipping container (Styrofoam box) with cold packs if the specimens will be delivered within 24 hr. These specimens should be shipped according to category B packing since these are primary diagnostic specimens and do not contain known biothreat agents.
5. Will my rapid flu test detect swine flu?
The sensitivity and specificity of rapid influenza kits for the novel Swine H1N1 virus is not known. CDC is evaluating capabilities of rapid test methods to detect the swine flu strains. Until that evaluation is complete, interpretation of results from the rapid flu tests may be unreliable. If there is clinical evidence of disease and strong suspicion of a “suspected case” with a negative test result, a specimen should be sent to the state public health lab. Contact your public health lab for what specimen criteria must be met before shipping to them.
6. Will my rapid shell vial tissue culture recover swine flu?
The sensitivity of the cell lines and mixed cell lines in shell vials and the immunofluorescent antisera used to detect swine flu H1N1 is not known. Contact the provider of your cells for documentation of the performance of their product. If there is clinical evidence of disease and strong suspicion of a “suspected case” with a negative test result, the specimen may be sent to the state public health lab. Contact your public health lab for what specimen criteria must be met before shipping to them.
7. Can rapid flu testing be done in our point of care labs?
Wherever possible manipulation of the specimen for testing should take place in a BSL-2 laboratory in a biosafety cabinet. Where that is not possible, such as a physician's office lab, then appropriate personal protective equipment (lab coat, gloves, masks, eye protection)should be worn when performing the test.
8. What precautions must be used in my viral lab?
CDC safety guidelines for labworkers states that diagnostic work for culture and typing of clinical samples from patients suspected to have swine flu virus should be conducted in a BSL-2 laboratory and testing performed in a biosafety cabinet. Similar precautions should be observed when preparing the specimen for diagnostic molecular testing.
9. Do all laboratory personnel need to wear enhanced personal protective equipment?
Personal protective equipment (PPE) is recommended based on risk. It would be prudent for laboratorians to wear the recommended respiratory protection, shoe covers, gown, eye protection and gloves if they are manipulating these specimens for diagnostic testing where aerosols may be created. Other personnel in the laboratory who are not handling these specimens would not require this level of PPE unless they are performing high risk activities such as mycobacterial culture.
The preferred respiratory specimens include: nasopharyngeal swab/aspirate or nasal wash/aspirate. If these specimens cannot be collected, a combined nasal swab with an oropharyngeal swab is acceptable. For patients who are intubated, an endotracheal aspirate should also be collected. Specimens should be placed into sterile viral transport media (VTM) and immediately placed on ice or cold packs or at 4°C (refrigerator) for transport to the laboratory.
2. If swabs are used to collect a specimen, which ones are acceptable?
There are a variety of swabs with a synthetic tip shown to have superior recovery of viruses, such as the flocked swabs. Avoid cotton tipped swabs, calcium-alginate swabs and those with a wooden shaft, which would inhibit the recovery of the virus, and may not be approved for use with the rapid testing kits.
3. If I receive a swab for rapid testing, I have nothing left to send for confirmation. What should I do?
You may ask your clinicians to collect two swabs. If your rapid test is positive for influenza A, then send the second swab to the public health lab for testing. Ideally the second swab should be immersed in viral transport media during transport. If only one swab is received, you may have leftover diluent where the cells from the swab were extracted that could be suitable for further testing. It is unknown at this time if these diluents or saline are compatible with the confirmatory tests.
4. I don’t have access to dry ice, how can I ship specimens to my public health lab?
It is acceptable to place the specimens in appropriately sealed shipping container (Styrofoam box) with cold packs if the specimens will be delivered within 24 hr. These specimens should be shipped according to category B packing since these are primary diagnostic specimens and do not contain known biothreat agents.
5. Will my rapid flu test detect swine flu?
The sensitivity and specificity of rapid influenza kits for the novel Swine H1N1 virus is not known. CDC is evaluating capabilities of rapid test methods to detect the swine flu strains. Until that evaluation is complete, interpretation of results from the rapid flu tests may be unreliable. If there is clinical evidence of disease and strong suspicion of a “suspected case” with a negative test result, a specimen should be sent to the state public health lab. Contact your public health lab for what specimen criteria must be met before shipping to them.
6. Will my rapid shell vial tissue culture recover swine flu?
The sensitivity of the cell lines and mixed cell lines in shell vials and the immunofluorescent antisera used to detect swine flu H1N1 is not known. Contact the provider of your cells for documentation of the performance of their product. If there is clinical evidence of disease and strong suspicion of a “suspected case” with a negative test result, the specimen may be sent to the state public health lab. Contact your public health lab for what specimen criteria must be met before shipping to them.
7. Can rapid flu testing be done in our point of care labs?
Wherever possible manipulation of the specimen for testing should take place in a BSL-2 laboratory in a biosafety cabinet. Where that is not possible, such as a physician's office lab, then appropriate personal protective equipment (lab coat, gloves, masks, eye protection)should be worn when performing the test.
8. What precautions must be used in my viral lab?
CDC safety guidelines for labworkers states that diagnostic work for culture and typing of clinical samples from patients suspected to have swine flu virus should be conducted in a BSL-2 laboratory and testing performed in a biosafety cabinet. Similar precautions should be observed when preparing the specimen for diagnostic molecular testing.
9. Do all laboratory personnel need to wear enhanced personal protective equipment?
Personal protective equipment (PPE) is recommended based on risk. It would be prudent for laboratorians to wear the recommended respiratory protection, shoe covers, gown, eye protection and gloves if they are manipulating these specimens for diagnostic testing where aerosols may be created. Other personnel in the laboratory who are not handling these specimens would not require this level of PPE unless they are performing high risk activities such as mycobacterial culture.
Saturday, May 2, 2009
A bird's eye view
This week's The Economist's insightful editorial on the pandemic follows the magazine's birds-eye view style. It correctly points to the next Winter as the main worry. That is, next month for countries in the southern hemisphere!. It contrasts the couple of hundred confirmed deaths so far attributed to the swine flu to the 30,000 deaths caused by the seasonal flu every year in the U.S., acknowledging that the "lack of proper tests" prevents an accurate mortality count in Mexico.
Will enough of the "proper" tests be available north of the border?
The "common" flu test: the rapid antigen test, itself in short supply these days, might not be of much help. The amplified molecular test is now available in Public Health labs, but these facilities could not possibly handle the demand. The Economist's editorial starts with the saying that no battle-plan survives contact with the enemy. In the plan to deal with the upcoming pandemic somehow we forgot to recognize that the thousands of hospital and private laboratories in the U.S., if equipped with the proper technology could, in short notice, change to the new primers and detection probes to fit the emerging flu virus recombinant and, within days, be ready to make a crucial contribution to containment efforts by providing the "proper" test.
Update: the CDC just issued a page listing Internet social tools related to the swine flu epidemic. Other web resources had been listed here.
Will enough of the "proper" tests be available north of the border?
The "common" flu test: the rapid antigen test, itself in short supply these days, might not be of much help. The amplified molecular test is now available in Public Health labs, but these facilities could not possibly handle the demand. The Economist's editorial starts with the saying that no battle-plan survives contact with the enemy. In the plan to deal with the upcoming pandemic somehow we forgot to recognize that the thousands of hospital and private laboratories in the U.S., if equipped with the proper technology could, in short notice, change to the new primers and detection probes to fit the emerging flu virus recombinant and, within days, be ready to make a crucial contribution to containment efforts by providing the "proper" test.
Update: the CDC just issued a page listing Internet social tools related to the swine flu epidemic. Other web resources had been listed here.
Thursday, April 30, 2009
Web resources on swine flu testing
Today, National Public Radio's Morning Edition commented on the prominent use of Internet resources in the unraveling swine flu pandemic. They mentioned the large number of followers of the CDC Twitt. The New York City Department of Health also has a Twitt, but it has not been updated since last Monday.
The U.S. Centers for Disease Control and Prevention (CDC) site is quoted most widely by on-line communities, such as the American Society of Microbiology's laboratory DivC discussion group.
In addition to Twitter, the CDC also offers a RSS feed. The CDC site includes a page discussing available rapid flu tests. The Federal Drug Administration (FDA) swine flu page offers e-mail updates and includes information on how to interpret the molecular (rRT-PCR) test for presumptive confirmation of the disease.
The World Health Organization swine flu site also offers a RSS feed. Medscape's swine flu alert center page has links to news, clinical reviews and articles.
Technical information about the CDC molecular test, such as specific target sequences, sample interference, performance with samples other than those collected in viral transport media, etc are not prominently available yet. In the meantime, the National Center for Biotechnology Information is gathering viral isolate sequences at breathtaking speed. Virologist Ruben Donis from the CDC, discussed molecular aspects of the swine flu strain in a ScienceInsider interview yesterday.
The U.S. Centers for Disease Control and Prevention (CDC) site is quoted most widely by on-line communities, such as the American Society of Microbiology's laboratory DivC discussion group.
In addition to Twitter, the CDC also offers a RSS feed. The CDC site includes a page discussing available rapid flu tests. The Federal Drug Administration (FDA) swine flu page offers e-mail updates and includes information on how to interpret the molecular (rRT-PCR) test for presumptive confirmation of the disease.
The World Health Organization swine flu site also offers a RSS feed. Medscape's swine flu alert center page has links to news, clinical reviews and articles.
Technical information about the CDC molecular test, such as specific target sequences, sample interference, performance with samples other than those collected in viral transport media, etc are not prominently available yet. In the meantime, the National Center for Biotechnology Information is gathering viral isolate sequences at breathtaking speed. Virologist Ruben Donis from the CDC, discussed molecular aspects of the swine flu strain in a ScienceInsider interview yesterday.
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