Microbiology Laboratory, City Branch of Oblast Lab Center (GCA) Laboratory Assessment Report November 2020

Contacts: [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]

Acronyms and abbreviations BSC Biosafety Cabinet BSS Basic Safety Standards ELISA Enzyme-linked immunosorbent assay EQA External Quality Assessment GCA Government Controlled Area IFU Instruction for Use IQC Internal Quality Control ISO International Organization for Standardization LIMS Laboratory Information Management System PCR Polymerase Chain Reaction PHC Public Health Center PPE Personal protective equipment PTS Professional Testing Scheme RNA Ribonucleic acid RT-PCR Reverse Transcription Polymerase Chain Reaction SOP Standard Operating Procedure/s UPS Uninterruptable Power Supply ULTFs Ultra-Low Temperature Freezer WHO World Health Organization

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Table of Contents Acronyms and abbreviations ...... 2 I. Overview ...... 4 II. Background ...... 5 III. Objective of the assessment ...... 5 IV. Methodology ...... 5 V. Team composition ...... 5 V. Results ...... 5 Organization and management ...... 5 Documents ...... 6 Specimen collection, handling and transport ...... 7 Data and information management ...... 7 Consumables and reagents management ...... 8 Equipment management ...... 8 Availability of equipment ...... 9 Facilities ...... 10 Human resources ...... 10 Biorisk management ...... 10 Public health functions ...... 11 SARS-CoV-2 testing capacity and capability ...... 12 V. Conclusions/Recommendations ...... 13

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I. Overview

550 000 280 1750 MOH/Public health

Estimated population Average number of Average number of type of laboratory covered by the specimens tested per PCR or RT-PCR tests run per week Laboratory day

Key indicators

Organization and management 95%

Document management 85%

Specimen collection, handling and transport 86%

Data and information management 100% Consumables and reagents management 95%

Equipment management 100% Facilities 76% Human resources 77% Biorisk management 87% Public health functions 95% SARS-CoV-2 testing capacity and capability 81%

Strengths Weaknesses

 Implementation of QMS and presence of ISO 17025:2019  There is lack of verification procedures for test kits and for accreditation certificate equipment  Biosafety & biosecurity requirements are in place.  LIMS is not available  New PCR Laboratory (since September 2020)  Old furniture, which needs to be replaced  The lack of educational trainings

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II. Background With the recent increase spike of COVID 19 cases in conflict affected zones, impact on overwhelming of laboratories and testing facilities in (Government Controlled Areas) is more and more concerning. A rapid assessment is urgently needed to assess the functionality of the laboratories, also in terms of quality of the work, to identify strengths and gaps and develop a plan of action. The assessment was carried on by WHO experts under the coordination of Health Cluster based on existing and pre-validated tools.

III. Objective of the assessment This report is focused on the analysis of the current state of Microbiology Laboratory of Kramatorsk City Branch of Donetsk Oblast Laboratory Center of MOH. It is the part of rapid assessment, which designated COVID-19 laboratories aims to assess: structure, equipment, quality of the work, HR and training needs, existing plans and protocols, gaps and major areas that require investment and response. The purpose is to produce an evidence-based plan of action.

IV. Methodology The assessment was conducted using WHO tool designed to assess capacities of existing laboratories which have implemented or aim to implement SARS-CoV-2 testing. Questionnaire is divided 2 parts: 1. Core capacities of the laboratory (which might include but are not limited to SARS-CoV-2 testing) 2. Specificities related to SARS-CoV-2 testing The direct visit to the laboratory was performed in November 2020.

V. Team composition The assessment was coordinated by joint efforts of Health Cluster assessment team and WHO. The team was composed of:

 Assessment was conducted by Artem Skrypnyk  Coordination was supported by WHO and Health Cluster: Emanuele Bruni, Igor Novykov  Design, analysis & reporting: Iryna Koval and Oleksandra Abrosimova

V. Results Organization and management

The laboratory normally works 38,5 hours in a week and the time could be extend due to providing emergency services. There are no shifts used, due to lack of staff. In terms of external

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communication: the telephone and fax are used, as well as computer with Internet access. There is a developed organizational structure with responsible laboratory staff and lines of authorities.

The laboratory reported that the salaries are rather small in health sector, including labs. The budget for consumables, test, and sample collection kits is not enough to cover all of the needs. The budget for purchasing/maintenance of equipment for surveillance and overall public health activities is adequate.

The laboratory received a certification ISO 17025 accreditation and undergone assessment by third party within the last 2 years. It was also reported that biologists (who forms the half of the PCR lab workforce) do not receive increase of the salaries due to COVID-19 hardship like personnel with medical background.

Lab is preparing for accreditation for ISO 15189.

Documents

The laboratory has an archiving system and the documents are retrievable. The manual describing the quality system is present in the laboratory. The lab has new PCR lab, but not all of the procedures are printed and handed over to staff. Personnel is generally trained on methods and use IFUs from the kits. Current versions of published standards, specimen handling, testing procedures (RNA extraction, RT-PCR, serology, etc.), and other similar documents are available in the laboratory. The procedure of storage of primary specimens, verifications of methods is in place, as well as the procedure to record incidents and complaints. Currently, the procedure for storage of COVID-19 primary/tested samples is not clear. Risk assessment related to the COVID-19 procedures has not been performed and documented. BSS procedures are reflected in the documentation1. For COVID-19 verification of the test results the procedure is following: 5 positive and 10 negative COVID-19 samples should be confirmed by Public Health Center or superior laboratory.

1 Subjects include next: handwashing, PPE, disinfection of contaminated materials, sterilization, glassware and equipment washing, waste disposal, laboratory cleaning, storage and destroy hazard sample, spillage, laboratory related injury, fire emergency.

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Specimen collection, handling and transport

Specific collection procedures used for specimens are partially documented. Internal system includes minimum patient identification details and standard specimen request forms are available. Specimen aliquots are traceable to the primary sample only with papers.

Very rarely the lab experiences problems with specimens from outside the lab. Staff is well trained the procedures on the quality of samples and documentation. The laboratory has developed criteria for acceptance or rejection of primary specimens. Primary specimens are adequately stored if not immediately examined. Adequate storing conditions as well as procedure for primary specimens2 are established in the lab. The lab reported the absence of enough capacity for ULTFs. Appropriate packaging for referring specimens is available. Transportation system for sample referrals is set-up, while trainings regarding transportation of infectious substances are not made.

Data and information management

The laboratory observations are recorded using paper logs. Before releasing, the results are reviewed and authorized. There is established procedure in case sample needs to be referred to another laboratory. There is an immediate notification of physicians when results are critical for patient care. It is also done when results are critical for ministry/surveillance network. The laboratory could provide statistical data from internal activities (f.e. number of tests ordered, aggregated qualitative/quantitative data, etc.). The laboratory reported that patients` information is protected and a back-up procedure is in place. LIMS is not available in the lab, but it is needed as laboratory processes up to 500 samples daily (COVID-19).

2 Storing in the fridge, -20C freezer, -70C freezer, or other recommended storage conditions.

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Consumables and reagents management

There is a person responsible for the procurement of consumables and reagents. The lab did not experience issues with reagent delivery. There is an inventory system for consumables and reagents. They are inspected upon receipt; and appropriately stored (with needed temperature, humidity, etc.). Reagents and kits have clearly written date of opening. All new reagents are verified against old reagents or reference materials before the use. Verification is rarely done for PCR kits. The laboratory never use expired reagents. Disposable supplies like tips, plastic pipettes, and gloves are never reused. There is accurate system for the forecasting consumables and reagents, there are calculations done in Excel using formula to calculate future needs depending on the particular kits and average sample numbers.

Equipment management

There is equipment inventory with available name of the equipment, contact details of the manufacturer (or local supplier), condition (i.e. new, used) and maintenance activities for some equipment (except for PCR equipment). The laboratory has needed resources to perform nucleic acids extraction, serology, RT-PCR, as well as bacteriology. There is an assigned person in charge of

maintenance management. The equipment is maintained in a safe working condition. There is a daily monitoring and recording of temperatures and airflow in biosafety cabinets. There is daily monitoring of temperature for temperature-dependent equipment. The laboratory implements

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preventive maintenance program. The staff is fully trained and authorized before first using equipment.

Availability of equipment

Available functioning equipment necessary for SARS-CoV-2 testing

Available in a Available in the Available in the single copy amount of 2 amount of 3

- ELISA equipment - Autoclave (clean) - Biosafety Cabinet class II

(washer/incubator/reader) - Autoclave (dirty) - Freezer (-70 °C) - Nucleic acid automated - Water distiller extractor - PCR working station - Printer for laboratory work - Thermal cycler (Thermocycler, PCR Machine or DNA Amplifier; Real Time with 4 channels) - Vacuum pump

Available in the Available in the Available in the amount 4 amount of 5 amount of 6

- Vortex - Centrifuge (simple) - Computer for laboratory work - Micropipette 100-1000 µl - Microfuge - Multichannel pipette

Available in the Available in the Available in the amount of 7 amount of 12 amount of 13

- Micropipette 0.5 - 10 µl - Refrigerator - Freezer (-20 °C) - Micropipette 10 - 100 µl - Micropipette 20 - 200 µl -

All equipment is registered and maintained. The majority of equipment is certified, besides nucleic acid automated extractor.

The laboratory also reported unavailable equipment: - Extraction manifold - Micropipette 20 µl - Plexiglas screen

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Facilities

The general condition of the lab is good. Windows and doors are plastic, except for entrance door, fire exit is locked on the key. Furniture is very old, wooden and should be replaced. Heating, ventilation and air conditioner is available in the laboratory. Waste disposal is outsourced. The lab faces electricity interruption sometimes. The lab mentioned the absence of emergency electric generator. Key equipment is protected by UPS. The laboratory noted having an adequate size for its activities (441 m2). Available are should be further reorganized, particularly the sample receiving room and respective procedure. However, there are no separate rooms for master mixing, addition of nucleic acids, and thermocyclers; all 3 processes are conducted in 1 room.

Human resources

21 people composes laboratory team: 5 senior staff representatives, 9 laboratory technologists, 5 laboratory assistants and 2 representatives of administrative staff. Staff is competent to perform nucleic acids extraction, serology, RT- PCR and bacteriology. There is a periodical competency assessment of the personnel (self-assessments and PTSes). The head of lab received training on quality management and provides the training to the laboratory staff periodically. Staff received one 3-days training on biosafety and biosecurity. There is a need on trainings at biosafety, risk assessment, procedure and quality assurance regarding SARS-CoV-2 testing. Biorisk management

The laboratory reported having biosafety level 21. Disinfection and decontamination, as well as waste management procedures are implemented in the laboratory. There are enough separate disposals for infectious and non-infectious wastes, while waste for used solvents is absent.

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Rooms have different sinks for handwashing only (one per unit). There are BSCs available for manipulation samples. There are biohazard signs indicated on the doors of the rooms where microorganisms are handled. The door entry locks with security measures that prevent non relevant staff or visitors to enter the laboratory are not in place. Accident/incident and nonconformities related to biorisk are correctly managed. Lab coats and laboratory linens are washed at the lab. There is a washing machine. PPE are available in enough quantities for the work load and number of laboratory personnel. Staff adhere adequate PPE during work (not worn outside lab areas, no eating or drinking within lab, no open- toed footwear etc.). The laboratory has dedicated PPE for each PCR areas (extraction, mastermix, and amplification). Personnel has access to occupational health services and follows a regular testing for SARS-CoV- 2 as health workers.

Public health functions

The lab is not a SARS-CoV-2 national reference laboratory, but it is a part of national surveillance network. Microbiology laboratory is aware of designated national reference laboratories for SARS- CoV-2. Responsibilities and mandates are not clearly defined in terms of responsibilities of the laboratory in national preparedness and response to public health emergency. During assessment it was reported that, the lab will not take immediate actions before the instructions will come either from or from the local health authorities. The lab gives advice on specimen collection and transport practices from the field during the investigation of public health emergencies. The lab has a stock of emergency laboratory sampling kits (PPE, sample collection material, transport media, sample transport packaging). The lab refers specimens to a national reference laboratory for public health purposes (e.g. routine surveillance, outbreak investigation). Microbiology lab also receives clinical specimens from local

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laboratories for confirmation and other tests (only for ELISA; PCR is conducted only by the assessed lab). COVID-19-related reporting to public health authorities is established and implemented. There is a standardized document (in the form of Excel template) to report notifiable diseases or other events. It is filled daily and shared with local health authorities, and further with PHC.

SARS-CoV-2 testing capacity and capability

The lab reported the absence of a particular SOP for COVID-19 sample collection. Specimen handling and SARS-CoV-2 testing procedures (RNA extraction, RT-PCR, serology, etc.) are not available to staff. The testing procedure for SARS-CoV-2 has been verified before starting regular testing. The laboratory use current versions of published standards for SARS-CoV-2 testing. To report results on SARS-CoV-2, Excel templates are submitted daily to local health administration and further to PHC. Risk assessment related to the procedures undertaken for SARS-CoV-2 testing is not in place. Biosafety manual is partially available, but it needs to be updated because of new PCR lab operating. Appropriate PPE for the handling and testing of specimens for SARS-CoV-2 are available. Appropriate PPE for handling and testing of specimens for SARS-CoV-2 is available. Personnel is trained in running SARS-CoV-2 testing with the help of such platforms as RT-PCR, Bio-Rad CFX96, Quant Studio 5 (will arrive soon). The equipment used for SARS-CoV-2 testing is adequately maintained. Required reagents for SARS-CoV-2 testing and the necessary consumables are available. IQC is included only if available in the commercial kits. The lab participates in EQA for the SARS- CoV-2 test and the system to record and assess EQA results is present. Assessed laboratory may ask PHC for referring specimens for confirmation of the results, but there is no guarantee that PHC will accept it. PHC refuses to receive samples from the fields as they are overburden. Personnel is trained in troubleshooting SARS-CoV-2 PCR results and a change in assay performance.

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V. Conclusions/Recommendations

The laboratory might implement: 1. Autoclaves are recommended to be replaced as soon as possible. 2. The wooden furniture is recommended to be replaced. 3. The contingency plan for preparedness and response to public health emergency should be developed, where the responsibilities and mandates of the laboratory mush be defined.

Next steps might be done by partners/WHO: 1. Trainings on transportation of infectious substances, verification/validation procedures, quality assurance, biosafety needs to be conducted. 2. Support in purchasing Laboratory information system. 3. Support in purchasing the higher power generator.

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