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12th April 2012
Healthlink
The National Healthlink Project provides a web-based messaging service which allows the secure transmission of clinical patient information between Hospitals, Health Care Agencies and General Practitioners.
The National Virus Reference Laboratory (NVRL) are pleased to announce that Virology results can now be accessed securely through Healthlink. For more information click on http://www.healthlink.ie/contact.htm or http://www.healthlink.ie/index.htm
2nd August 2011
Introduction of HIV-1 Genotvpic Integrase Resistance Testing
We have recently introduced HIV-1 genotypic integrase resistance testing to the antiretroviral susceptibility test repertoire at UCD NVRL.
Raltegravir is the only integrase inhibitor licensed for use in treatment of HIV-1 infection. A second member of this drug class, elvitegravir, is in the late stages of clinical development. Resistance toraltegravir has been shown to emerge rapidly in cases of suboptimal background therapy with 3 common resistance pathways, namely Y143, Q148 and Ni 55. However, more than 20 resistance associated mutations have been described. Recent clinical trials indicate that resistance to raltegravir will confer resistance to elvitegravir and vice versa.
The HIV-1 genotypic integrase resistance service at the NVRL will complement the protease and reverse transcriptase resistance tests and the genotypic tropism assay thus providing a comprehensive menu to clinicians treating HIV-1 infection. At least 1ml plasma from patients with a HIV-1 viral load >1,000copies/ml is required to generate a result. The expected turnaround time is 14 working days. Request forms are available to download at www.nvrl.ie
If you have any queries about the above service please do not hesitate to contact me, Dr Cillian De Gascun or Dr. Suzie Coughlan.
25th July 2011
Change in Hepatitis C genotyping at the NVRL
The NVRL will replace its current HCV genotyping assay - the Siemens Versant HCV genotyping v2.0 (Lipa)- with the Abbott RealTime HCV GT-11 assay in July 2011.
The Abbott RealTime HCV GT-II is a CE marked automated real time RT-PCR assay designed to determine genotype in HCV infected individuals. The system distinguishes between genotypes 1-6 with an estimated sensitivity of 5001U/ml. The system offers a number of analytical and procedural advantages over the current assay resulting in an anticipated reduction in result turnaround time.
However, a minimum of 1ml plasma or serum, separated from whole blood and frozen within 6 hours, is required for the Abbott real-time assay. Therefore, centres wishing to determine both HCV viral load and HCV genotype are advised to collect and process two (2x1ml) separate blood samples from the patient in order to ensure sufficient volume for both tests.
If you have any queries about this new assay please contact me or a member of the NVRL clinical team on 01 716 1236/1240/1349/1359.
14th February 2011
NVRL launches IL28B Genotyping - a support tool in the treatment of Hepatitis C infection
The NVRL has added IL28B genotyping to the repertoire of tests at the NVRL.
Recent genome wide association studies identified IL28B genetic polymorphisms as strong predictors of spontaneous clearance of Hepatitis C virus (HCV) and response to peglFNa and ribavirin combination therapy in HCV genotype 1 infected individuals. Subsequent studies showed that combination peglFNa and ribavirin therapy in these patients was 2- to 3-fold more likely to be successful if patients were carriers of the CC (rs12979860) genotype as compared with either CT or TT genotypes. IL28B genotype was the strongest predictor of sustained virological response, showing a higher odds ratio (OR = 5.2) than any of the other independently associated predictors of treatment response such as baseline viral RNA levels, fibrosis stage or ethnicity.
IL28B polymorphism genotyping should ideally be requested pre-treatment in conjunction with baseline HCV RNA loads and HCV genotype to provide a comprehensive assessment of the likelihood of treatment response. The NVRL report will document the presence of the CC genotype or the alternative CT or TT genotypes.
Please note that this test involves characterisation of a fragment of the human genome and therefore the ethical implications of this investigation should be considered by your institution before routine test requesting commences. Indeed, patient consent may be advisable.
If you would like more information regarding this service, please contact me or a member of the NVRL clinical team at 01 7161236/1240/1349.
11th January 2011
Discontinuation of complement fixation testing for Mycoplasma, Chlamydia and Coxiella from February 1st 2011.
Commencing February 1st 2011, the NVRL will no longer perform complement fixation tests (CFT) for the diagnosis of the above bacterial infections (PCR for C.trachomatis will continue as normal ). There are a number of reasons for this decision.
Over the past 6 months, the NVRL – in conjunction with laboratories in the UK – has been unable to obtain control antigens for Chlamydia for use in the CFT assay due to a manufacturing problem. Unfortunately, no alternative source of antigen is available. This issue is unlikely to be resolved imminently, and as there has been limited demand for testing in CFTs absence, the NVRL cannot justify retaining this test in the current financial climate.
In relation to Mycoplasma testing, the NVRL has completed a review of CFT versus IgM EIA for the past 12 month period. This review revealed that the overall demand for Mycoplasma CFT was low, and that CFT provided minimal additional diagnostic value to Mycoplasma specific IgM testing. As a consequence, CFT testing will be discontinued, and the NVRL will move to introduce Mycoplasma specific IgG testing in addition to retaining the current IgM assay.
Finally, the demand for Coxiella burnettii testing in conjunction with the very low number of significant results means the retention of CFT cannot be justified on the basis of this pathogen alone. Therefore, we are recommending that future samples be sent directly from your laboratory to the UK HPA for Coxiella testing
- Bristol Regional HPA Laboratory (Coxiella Serology), Department of Microbiology, Myrtle Road, Kingsdown, Bristol BS2 8EL
While we appreciate this change in practice may cause some initial mild disruption, we believe it will result in shorter turn-around times, more efficient use of available resources, and therefore an overall improvement in patient care.
If you have any questions regarding this change in policy, please do not hesitate to contact the staff in the NVRL.
Note of Clarification:
Please note, the above notification relates to Chlamydia pneumoniae testing as part of the Atypical Pneumonia screen on blood specimens and does not affect the Chlamydia trachomatis test performed on urines/swabs as part of the STI screen.
8th February 2010
On-call Service for PandemicA(H1N1)2009
We would like to advise NVRL users that from the weekend of the 6th & 7th February 2010 our on-call service for pandemic flu detection will cease operation. If you wish to speak to one of our clinical staff regarding this issue, please contact Suzie Coughlan or Jeff Connell at the NVRL. Our clinical mobile number is 087 9806448.
30th October 2009
NVRL testing policy for hospitalised patients with suspected Pandemic H1N1 2009
- Respiratory specimens* requested for H1N1 investigations will be tested using a real time RT-PCR for seasonal Influenza A and B and a specific test for Pandemic H1N1.
- The turnaround time is 24 hours for 90% of hospitalised patients. Weakly positive samples may take longer to confirm.
- The routine diagnostic service is Monday to Friday 8am to 5.30pm. All positive results will be phoned to the requesting clinician or to designated personnel in the Microbiology laboratory (full contact details of the requesting clinician must be provided to the laboratory to ensure prompt reporting of test results). Samples should reach the UCD NVRL by 11am to be processed that day.
- Results are available Monday to Friday at 01 7161323, 7161358 or 7161341
- An “out of hours” service for urgent cases is available on Saturday and Sunday. Access to this service is ONLY through the clinical on call team at the NVRL at 087 9806448. Samples must arrive to the laboratory before 1pm to be processed that day. All results processed out of hours will be phoned to the requesting clinician or to designated personnel in the Microbiology laboratory.
*Nasopharyngeal swabs, nasopharyngeal aspirates, bronchiolar lavages or respiratory secretions are recommended especially when lower respiratory tract infection is suspected. Combined nose and throat swabs are also suitable although the sensitivity may be reduced due to the variability in sample collection.
22nd July 2009
NVRL Influenza A(H1N1)v Laboratory Test Schedule during early phases of mitigation
Due to the high number of samples received for Influenza A(H1N1)v testing we have revised our laboratory testing schedule which is outlined below.
• Laboratory testing of respiratory samples for Influenza A (H1N1)v is carried out daily. Samples need to arrive to the laboratory by 11am in order to be processed that day.
• The turnaround time for results for Influenza A (H1N1)v is 72 hours from receipt of the sample. Turnaround times are subject to volumes of testing and may be revised. In addition the 72 hour TAT may be exceeded in cases of weakly positive samples.
• The NVRL will telephone positive or probable results to the requesting clinician. Full contact details of the requesting clinician must be provided to the laboratory to ensure prompt reporting of test results. Treatment should not be withheld while awaiting laboratory confirmation. Please refer to HPSC Guidelines for management of persons with Acute Febrile Respiratory Illness who may have Influenza A (H1N1).
• A hard copy of results will be issued to requesting clinicians within 96 hours of receipt of sample.
• For patients with serious clinical manifestations weekend testing is available and can be accessed through the clinical team (087 9806448).
A copy of the NVRL Influenza Test Request Form can be downloaded here . The Procedure for Packaging & Transport of Specimens can be downloaded here
More information on Swine Flu is available here
(Adobe Reader is required to open and print these forms. It can be downloaded by clicking the link below.)
August 2008
Introduction of combined Chlamydia trachomatis/ Neisseria gonorrhoeae testing in the NVRL
The NVRL is currently changing its platform for the molecular investigation for Chlamydia trachomatis (CT). The Roche COBAS Amplicor CT assay will be replaced with the Gen-Probe Aptima Combo2 assay (to be performed on the Tigris platform) from August 4th of this year. The Aptima assay targets ribosomal RNA (rRNA) rather than DNA. The reasons for this change are as follows:
- The new Aptima Combo2 assay is very sensitive and is capable of detecting the recently described Swedish variant of Chlamydia trachomatis
- In addition, the new platform is fully automated with DTS (direct tube sampling) and therefore possesses a greater specimen capacity. It is envisaged that a shorter turnaround time will result when the new platform is fully operational.
- Finally, a separate confirmatory test is available on the Aptima platform for all samples testing positive, thereby improving the accuracy of the results
There are two issues we would like to highlight for you on the introduction of this new assay:
- The Aptima assay comes with its own specimen collection devices. These will be available directly from the NVRL and requires no special conditions for transport or storage. (Please refer to the attached instructions for the submission of diagnostic CT specimens using new collection devices, see below). Orders for specimen collection devices can be made via email or fax, details of which are provided below.
- As suggested by the name (Aptima Combo2), this assay is a dual kinetic assay that detects both CT and Neisseria gonorrhoeae (gonococcus/GC) in a single swab/ urine sample concurrently. With the increasing prevalence of sexually transmitted infections in Ireland, this combined approach to the molecular diagnosis of CT and GC is advisable and may become best practice in many sexual health clinics. Please note the addition of GC testing will not impact on CT specimen turnaround times.
Neisseria gonorrhoeae (GC) testing:
Whilst bacterial culture remains the gold standard for the diagnosis of GC infection, and is also of great importance for detecting the emergence of antimicrobial resistance, the Aptima Combo2 assay provides a mechanism for screening large numbers of patients conveniently, rapidly, and effectively. This is especially the case for asymptomatic patients. However, for symptomatic patents, it is anticipated many centres will continue to send specimens for bacterial culture in addition to molecular testing.
Reporting of Results:
1. The reporting of results for CT will remain essentially the same. However, there will henceforth be two results listed for all positive specimens. This is on account of the new confirmatory assay (the result of which will also be reported) that the Gen-Probe platform provides. Of note, the report comment will report the detection (or not) of Chlamydia trachomatis rRNA rather than DNA. A clinical comment will also accompany positive results.
2. Positive GC results will report the detection of Neisseria gonorrhoeae rRNA, and recommend collection of a further sample for bacterial culture and antimicrobial susceptibility testing. Please note this comment does not reflect a lack of confidence in the assay, it merely reflects the need to monitor antimicrobial susceptibilities where feasible for surveillance and treatment purposes.
Obtaining Specimen Collection Devices
There are two specimen collection devices (SCD) available for the new Aptima assay, one for urine samples and the other is a unisex swab device for urethral and cervical samples.
A significant advantage of these new SCD is that both are stable following urine/swab collection at room temperature for a period of thirty days. This will negate the need for refrigeration or urgent transport of samples to the NVRL.
SCD can be ordered in boxes of fifty and have a shelf-life of approximately nine months (expiry date printed on the side of each SCD). We would anticipate delivering an initial supply of SCD in the week beginning July 21st. Subsequent orders of SCD can be made my emailing nvrl@ucd.ie or faxing (01) 716 1135. When emailing or faxing, please place the word “Chlamydia” in the subject line so your order can be dealt with promptly.
In conjunction with the first SCD delivery, we attach Gen-Probe Specimen Collection Guides illustrating the use of the new SCD (see below).
If you have any other queries or feedback about this new assay please feel free to contact Dr Suzie Coughlan on 716 1359, Dr Cillian De Gascun on 716 1240, or Dr Jeff Connell on 716 1321.
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