Check List for Annual WHO Accreditation

Check List for Annual WHO Accreditation

Polio Sequence Laboratory

Check List for Annual WHO Accreditation

Introduction

Detection and laboratory evaluation of acute flaccid paralysis (AFP) at an annual non-polio rate of >1/100,000 in children less than 15 years is the standard for certifying polio eradication for all countries. Tests for virus isolation are performed on two adequate stool specimens collected within 14 days of onset of paralysis, and 24-48 hours apart, from each AFP patient. Supplemental virus surveillance may consist of specimens from contacts of AFP cases, special surveys of healthy children, and the environment, as appropriate. Test results are accepted only from a WHO accredited Poliovirus Laboratory.

In laboratories supporting the Polio Eradication Initiative, polioviruses from AFP cases or other sources are routinely characterized to determine virus serotype and intraype according to methods recommended by the World Health Organization (WHO) and described in Polio Laboratory Manual WHO/IVB/04.10 and at the website The nucleotide (Nt) sequenceof the complete VP1 region of the Poliovirus genome is also determined for all non-Sabin polioviruses and isolates that give inconclusive results in intra-typic differentiation tests. VP1 Nt sequence results are interpreted to make inferences about virus transmission links, surveillance sensitivity and accuracy of laboratory results during previous stages of testing.

Accreditation provides documentation that a laboratory has the capacity to accurately generate, interpret and promptly report complete VP1 Nt sequences of poliovirus isolates.

Accreditation is reviewed annually by WHO and is based on Laboratory performance during the preceding 12 months with complete data, usually, from 13 months to 1 month prior to evaluation. Selection of the most recent 12-month period provides an assessment of current performance and permits review of Laboratories at any time during the calendar year.Accreditation is given for the upcoming calendar year.

Fourcriteria for accreditation:

1. At least 25 polio or non-polio entero virus (NPEV) isolates are sequenced annually.

Active laboratories should maintain proficiency and expertise to perform the relevant procedures for sequencing and interpreting of results. Ideally sequencing should be performed throughout the period reviewed for accreditation, and analysed isolates should be obtained from samples sources that are relevant to the polio eradication initiative (AFP cases, contacts, sewage samples etc.). In polio-free or IPV using countries, laboratorymay have insufficient polio viruses referred for analysis. In such situations sequences from NPEV isolates can contribute to work performed to maintain analytical proficiency. Complete VP1 Nt sequences should be analysed for isolates from polio and NPEV isolates and CSF. Partial VP1 nt sequences of NPEV can be considered to contribute to workload to maintain proficiency in polio-free regions or IPV using countries. Seqeunces in VP1 region are specified for compatibility with the region of the genome that is analysed for polio virus surveillance.

1. Poliovirus VP1 nucleotide sequence results are reported to the Programme and the Regional Laboratory Coordinator for  80% of all polioviruses from AFP cases and contacts within 7 days of receipt or detection of such isolates in the same laboratory.
2. This criterion applies to Non-Sabin like (NSL) polioviruses and isolates that give inconclusive results in intratypic differentiation (ITD) tests. Isolates can be obtained from various sample sources, but those from AFP cases and their contacts should be given highest priority for testing. The target time for reporting sequence results is 7 days.

- In the case of PV outbreaks, the timeline must be met for the first wild poliovirus detected for the outbreak; for the first case in the first administrative region (e.g. province) of the country; and, for any "hot cases" specified on the case investigation form accompanying the specimen sent for analysis.

- The reporting time will be waived for only the exceptional situations in which alternatives to the standard sequence primers are needed to obtain valid sequences.

1. The score is  90% on the most recent WHO poliovirus sequencing proficiency test (PT).

PT results must be reported within 7 days of panel receipt to receive full credit.

The score from the annual on-site review of laboratory operating procedures and practices is 90%.

For Laboratories with high annual accreditation scores for 3 or more consecutive years and with no significant changes in management personnel during that period, the Global Laboratory Coordinator may waive the on-site review upon satisfactory completion of the annual checklist by the Laboratory.

Laboratories that perform test procedures other than those recommended by WHO should provide documentation that such procedures, when used in their laboratories, are equivalent in specificity and sensitivity to WHO poliovirus procedures.

A Laboratory that achieves less than the passing score on any one of the applicable fourcriteria will work with the WHO Global or Regional Laboratory Coordinator to:

• Identify areas where improvement is needed.
• Develop and implement a work plan.
• Monitor laboratory progress.
• Provide for additional PT tests where required.
• Provide for re-testing when required.
• Continue follow-up steps to achieve full accreditation.

A Laboratory that fails to achieve passing PT testing scores within 6 months of the annual review is deemed non-accredited and must arrange in collaboration with WHO for an accredited Laboratory to perform duplicate tests on all specimens.

The checklist consists of four parts. Part I summarizes the findings of the review and the data on which accreditation is based. Part II records Laboratory performance for criteria #1 through #4. Part III provides a profile of the Laboratory. Part IV is a checklist for evaluation of laboratory operating procedures and practices for criterion #4.

This checklist is intended as a guide. The experienced reviewer is expected to be flexible, ask detailed questions and make recommendations as appropriate to assure high quality laboratory performance.

Polio Sequence Laboratory

Check List for Annual WHO Accreditation

Laboratories are to be notified in advance of the accreditation review and provided with a copy of this form to assist in gathering information.

Dates of Review: / Accreditation for Calendar Year:
Address:
Phone: / Fax: / Email:
Head of Department:
Head of Laboratory:
Technical Supervisor:
Reviewers:
Name of National Accrediting Authority and current accreditation status:

Recommendations (check one):

 / Accredit: Laboratory meets all criteria
 / Provisionally accredit: Laboratory passed the most recent proficiency test, but failed to achieve one or more of the remaining criteria
 / Do not accredit: Laboratory did not pass the most recent proficiency test

Part I: Summary of Review

Nucleotide sequences are generated and analysed on site for at least 25 Poliovirus or Non-Polio Enterovirus isolates annually
Complete VP1 nucleotide sequence results on 80% of poliovirus isolates are reported within 7 days: / %
The score is  90% on the most recent WHO poliovirus sequence proficiency test (PT): / %
The score on annual on-site review is at least 90%: / %
SUMMARY, COMMENTS AND RECOMMENDATIONS:

Part II: Laboratory Performance In Previous 12 Months

Date: (dd/mm/yy) to(dd/mm/yy)

Total number of Polio or Non-Polio Entero Virus isolates from all sources with nucleotide sequence obtained and analysed on-site (Target 25): / Total number of isolates
1.1. / Source and number of Poliovirus isolates sequenced:
No. Polio / No. NPEV
From AFP cases:
From contacts of AFP cases:
From immunodeficient persons:
From non-AFP patients (specify diagnosis):
From sewage specimens:
From other specimens (specify):
1.2. / Source and number of RNA specimens obtained directly from clinical specimens:
No. sequenced / No.
Polio
Number of RNA specimens from clinical sources (specify source):
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Percentage of VP1 nucleotide sequence results for poliovirus isolates from AFP cases and contacts that are reported on time to the Programme and the Regional Laboratory Coordinator (Target 80%): / Score: / %
2.1. / Number of poliovirus isolates from AFP cases and contacts received for sequencing (exclude duplicates):
2.2. / Number of poliovirus isolates from AFP cases and contacts with total VP1 nucleotide sequence reported within 14 days:
2.3. / Number of poliovirus isolates from other sources (e.g. sewage samples or other clinical specimens) with total VP1 nucleotide sequence reported within 7 days of detection:
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Score of the most recent poliovirus sequence
proficiency test (Target 90%):
Procedure
Evaluated / Date PT
Received / Date PT
Reported / Score
For PT
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Score for the on-site review. (See Section 4. Target 80%).

Part III: Laboratory Profile

Staff
1.1. / Number of scientific and technical staff assigned to molecular or sequence laboratory. Please list according to function, indicating years of experience and proportion of current working time spent on polio-related activities:
Names of staff / Position Title and Specific Duties / Full-time or Part time / % of time spent on Polio work / Years of experience in Polio Lab
COMMENTS AND RECOMMENDATIONS:
Space allocation (Provide floor plan or sketch of laboratories showing equipment layout and workflow):
2.1. / Total area (square metres) available:
2.2. / Number of rooms:
2.3. / Separate and sufficient space is allocated for carrying out laboratory, office and data management processes:
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:

1. Reference Laboratory activities performed for Global Polio Eradication Initiative

3.1. / Countries/Laboratories submitting specimens and/or isolates for testing
Name ofCountry/Laboratory / No. Stool specimens referred for testing / No. virus isolates
referred for testing
3.2. / Training activities performed:
Describe training activities performed and number of personnel trained:
3.3. / Reagents, materials, and supplies provided or distributed:
Describe and quantify any reagents and supplies distributed to other laboratories:

Part IV: Laboratory Operating Procedures and Work Practices

1. / Management and Supervision (8%): / Score / %
1.1 / The lines of supervision and accountability are clear to all staff.
1.2. / An organizational chart is available
1.3. / Arrangements are made for qualified back-up staff to sustain services during scheduled staff absences (e.g. vacation, study, maternity or paternity leave):
1.4. / Periodic meetings are held with staff to review and improve laboratory performance:
1.5. / Standard Operating Procedures have been developed and arrangements are in place for periodic review, update and evaluation of compliance:
1.6. / There is signed evidence that supervisors critically review test worksheets and results for accuracy and completeness, and indicate need for any follow up actions:
1.7. / The supervisor ensures that sufficient supplies, reagents and functional equipment are available to handle the laboratory's workload:
1.8. / Mechanisms are in place for staff training, periodic update of staff on technical issues and monitoring of work performance to verify technical skills:
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Staff (5%): / Score / %
2.1. / Staff are effectively assigned:
2.2. / Current duties and responsibilities of staff are specified in written job descriptions:
2.3. / The number of trained staff is adequate to handle the workload:
2.4. / Technical staff have had specific training on poliovirus sequencing, interpretation, and reporting requirements for the Polio Eradication Initiative:
2.5. / Staff training records are available and kept up-to-date:
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Utilization of Space (3%): / Score / %
3.1. / Physical layout allows for separation of rooms or work areas used for the main required processes: reagent preparation, sample preparation, nucleic acid amplification / sequencing, and post-amplification / sequencing analytical processes.
3.2. / Separate work areas or bio safety cabinets (class II) are used for handling infectious and non-infectious materials.
3.3. / There is a unidirectional flow of materials and equipment from areas where work is carried out on non-amplified to areas where amplified nucleic acid materials are manipulated.
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Equipment (4%): / Score / %
4.1. / Equipment manuals and written standard operating procedures are available:
4.2. / A current inventory of equipment is maintained:
4.3. / Equipment is calibrated periodically, as appropriate:
4.4. / Equipment is maintained periodically as recommended, dates recorded and maintenance records are kept:
4.5. / Equipment is functioning, and in good condition:
4.6. / Equipment location is conductive to optimal performance:
4.7. / Non-functional equipment that cannot be repaired are labelled as such and removed from the laboratory area:
4.8. / Equipment used in performing nucleic based techniques are sufficient in number:
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Prevention and detection of cross-contamination during nucleic acid amplification steps (12%): / Score / %
5.1. / Written standard operating procedures are available describing measures to be taken to prevent or detect cross contamination:
5.2. / Separate dedicated reagents, equipment and pipettors are available in pre-amplification and post-amplification work areas:
5.3. / Separate dedicated Personal Protective Equipment is available in sufficient quantity and used or worn in pre-amplification and post-amplification work areas:
5.4. / Aerosol resistant tips and positive displacement pipettors are used for any manipulations requiring use of pipettors:
5.5. / Any preparation of aliquots of isolates is carried out in the pre-amplification work area:
5.6. / Reagents are dispensed an stored in small volume aliquots:
5.7. / Caution is taken to avoid contamination of reagents, lab equipment and disposables with RNases when performing RNA extraction, including use of powder-free gloves, new plastic ware and DEPC treated glassware, as required:
5.8. / Master mixes of PCR reagents are prepared and subsequently dispensed into individual reaction tubes before the addition of specimens in areas free of amplified nucleic acid:
5.9. / Appropriate negative (i.e. no template or reagent only) controls are included in every PCR test run:
5.10. / Poliovirus isolates and unamplified positive control reference standards are stored in a separate work area and freezer to cDNA and amplified DNA products:
5.11. / Cleaning arrangements (e.g. wiping bench tops, floors, rack and pipettors with freshly prepared hypochlorite solution) are in place in the pre-PCR work areas and UV irradiation is used to minimize the risk of contaminating DNA in work areas in which amplified nucleic acids are generated or manipulated:
5.12. / Appropriate measures are in place for disposal of unneeded test materials or products:
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Documentation of reagents and methods used for sequencing:
Laboratory Process / Supplier and catalogue number for any commercial
product in use / Reference citation
for any
"in house" method" in use / Documentation available for validation of method on-site? (Yes/No)
RNA extraction
RT-PCR amplification primers
Purification of amplicon
Quantification of amplicon
Sequencing method
Removal of excess dye terminators
COMMENTS AND RECOMMENDATIONS:
Sequencing of Polio or Non Polio Enteroviruses (12%): / Score: / %
7.1. / Written standard operating procedures are available for performing sequencing:
7.2. / Complete VP1 nt sequences are generated on site for each Poliovirus that is analysed:
7.3 / Complete VP1 nt sequences is generated on site for each NPEV isolate or NPEV positive original specimen that is analysed. Alternatively,partial VP1 sequences are analysed for NPEVs:
7.4 / Information is available about primers used for amplification and/or sequencing, including source, primer sequence, primer target, lot number and dates of receipt and use:
7.5 / Heterotypic virus mixtures are directly sequenced using specific sequencing primers
7.6 / All homotypic virus mixtures are referred to GSL
7.7 / Single step cycle sequencing is used:
7.8 / Appropriate positive and negative controls are included in test runs for determining test validity and to assist with trouble shooting:
7.9 / Nucleotide sequences of both DNA strands generated by PCR are analysed:
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Analysis of sequences (20%): / Score: / %
8.1. / Written standard operating procedures are available for sequence editing, analysis, reporting and archiving:
8.2. / Computer software in use allows for assembly and viewing of outputs of multiple sequence runs, sequence editing, alignment and analysis:
8.3. / Laboratory has access on-site or via appropriate functional electronic communication mechanisms to sequences of appropriate reference strains for sequence comparison:
8.4. / Laboratory has on-site access to a database of VP1 Nt sequences of contemporary wild polioviruses in its geographical region oruses suitable communication mechanisms to share sequences or databases, as necessary,within 48 hours of detection with other regions to ensure appropriate and accurate sequence database searches for determining genetic relationships among viruses:
8.5. / Laboratory has the capacity to determine and report percentage Nt sequence homology to the closest genetic relatives of identified viruses either in the form of a matrix of relationships or summarized as a phylogenetic tree:
NATURE OF DEFICIENCY, IF ANY, AND DESCRIPTION OF CORRECTIVE ACTION:
COMMENTS AND RECOMMENDATIONS:
Biosafety practices and procedures (10%): / Score: / %
9.1. / Employees have been instructed in biosafety:
9.2. / Standard Operating Procedures are available for disinfection and decontamination of materials and surfaces, disposal of infectious wastes, clean up of spills, reporting of accidents and exposures to infectious materials:
9.3. / Guidelines have been developed and staff have been trained in emergency procedures to be used in case of fire or other disasters:
9.4. / Biosafety practices are enforced, including:
a. Hand washing:
b. Pipetting with aid of mechanical device:
c. No eating, drinking, smoking, or storage of food in laboratory:
d. Use of Personal Protective Equipment (PPE) such as gloves, laboratory coats, and face masks, as appropriate to the task performed:
e. Restricting use of laboratory coats and gloves to laboratory areas only:
f. Decontaminating all infectious or clinical waste before discarding:
g. Decontaminating laboratory work surfaces:
h. Use of puncture resistant, non-corrosive and autoclaveable containers of appropriate size for disposal of infectious wastes: