Laboratory Assessment Report November 2020

Toretsk City Branch of Donetsk Oblast Lab Center of MOH (GCA) Laboratory Assessment Report November 2020

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Acronyms and abbreviations BSC Biosafety Cabinet ELISA Enzyme-linked immunosorbent assay EQA External Quality Assessment GCA Government Controlled Area IQC Internal Quality Control ISO International Organization for Standardization LIMS Laboratory Information Management System MOH Ministry of Health 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 UV Ultraviolet WHO World Health Organization

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 ...... 6 Organization and management ...... 6 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 ...... 11 Public health functions ...... 11 SARS-CoV-2 testing capacity and capability ...... 12 V. Conclusions/Recommendations ...... 13

I. Overview

300 000 400 1128 MOH/Public health/ environmental/ Estimated population Average number of Average number of food safety/ covered by the specimens tested per PCR or RT-PCR tests type of laboratory Laboratory day run per week

Key indicators

Organization and management 88%

Documents 65%

Specimen collection, handling and transport 86%

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

Equipment management 92% Facilities 56% Human resources 69% Biorisk management 79% Public health functions 82% SARS-CoV-2 testing capacity and capability 71% Strengths Weaknesses

+ Strong data and information management, as well as  Outdated Biosafety manual consumables and reagents  Absence of LIMS  Absence of BSC  The lack of special trainings for the laboratory personnel

II. Background With the recent increase spike of COVID 19 cases in Ukraine conflict affected zones, impact on overwhelming of laboratories and testing facilities in Donetsk Oblast (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 Toretsk City Branch of Donetsk Oblast Lab Center of MOH (GCA). 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. Shifts are not used because of lack of staff. In terms of external communication: the telephone and computer with Internet access are available. There is a developed organizational structure with responsible laboratory staff and lines of authorities.

The laboratory reported that budget for salaries is adequate. Current situation with budget for equipment is following: it is much more than it is used to be before the pandemic, however it is still not enough to cover all the needs in equipment, reagents, and consumables needed for overall public health activities.

The laboratory received a certification ISO 17025 (2017 is available). Currently, the lab reported to be conducting process of accreditation for ISO 15189.

Documents

The laboratory has an archiving system and the documents are retrievable. The management of laboratory documents are available in the form of paper journals and Excel forms. The manual describing the quality system is present. Current versions of published standards, specimen handling, testing procedures (RNA extraction, RT-PCR, serology, etc.), and other similar documents are available in the laboratory, except all SOPs for COVID-19 PCR testing. Some manuals/kits inserts are available, but not translated or printed for immediate use. Documents are stored in the office of the head of the lab and might not be readily available for other personnel. The procedure of storage of primary specimens is following: positive results are archived and negative are autoclaved. Validation procedure is neither available, no performed. In the same time, verification procedure is available, but not performed. Procedure to record incidents is not in place.

Risk assessment related to the lab procedures has not been performed and documented. Biosafety procedures are partially written in the manual, but it needs to be updated. 1 Subjects like

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.

handwashing, storage and destroying hazards, as well as laboratory related injury and fire emergency are not addressed with the manual. Specimen collection, handling and transport

Collection procedures used for specimens are documented. The legislation is in place, but the lab does not have particular SOP for COVID-19 sample collection. Patient report form is standard and approved by MOH. Internal system includes minimum patient identification details and standard specimen request forms are available for use.

Specimen aliquots are traceable to the primary sample only with papers. Very rarely the lab experiences problems with specimens from outside the lab. There are no rejections of primary specimens due to political reasons. 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, but there is no separate procedure for COVID-19 samples. Appropriate packaging for referring specimens is available. There is no person responsible for the transport of infectious substances. Transportation system for sample referrals is set-up, while trainings regarding local & international regulations for transportation are not made.

Data and information management

The laboratory observations are recorded. 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 and relevant ministry/surveillance network. The laboratory could provide statistical data from internal activities (f.e. number of tests ordered, aggregated qualitative/quantitative data, etc.).

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

The laboratory reported that patients` information is protected and a back-up procedure is in place. The laboratory uses such softwares as Excel and BioRad. LIMS is not available in the lab.

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. Different PCR kits are verified, but batch to batch verification is not conducted for PCR kits. Concerning COVID-19 PCR kits, they are not validated. All test results are recorded and reported in a standardized format. Paper system is used in combination with the Excel based system. Average number of specimens tested in serology per week is 450 ELISA.

The laboratory never uses expired reagents. Disposable supplies like tips, plastic pipettes, and gloves are never reused. There is system for the forecasting needs for consumables and reagents.

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. The laboratory has needed resources to perform nucleic acids extraction, serology, RT-PCR. There are available incubators, dilutor, water bath, microscopes, express-testing of water, pH-meters. 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 for temperature-dependent equipment. The

laboratory implements preventive maintenance program. BSC is not available in the laboratory. All manipulations are conducted on the open bench. Preventive maintenance program is in place. The staff is duly trained and authorized before first use of 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

- Nucleic acid automated - Autoclave (clean) - Centrifuge (simple ) extractor - Autoclave (dirty) - Vortex - ELISA equipment - Microfuge (washer/incubator/reader) - Micropipette 10 - 100 µl - Extraction manifold - Micropipette 20 - 200 µl - Freezer (-70 °C) - Multichannel pipette Vacuum pump - - PCR working station - Water distiller - Thermal cycler (Thermocycler, PCR Machine or DNA Amplifier; Real Time with 4 channels)

Available in the Available in the Available in the amount 4 amount of 5 amount of 12

- Freezer (-20 °C) - Computer for laboratory work - Refrigerator - Micropipette 20 µl - Printer for laboratory work - Micropipette 0.5 - 10 µl - Micropipette 100-1000 µl - - All equipment is registered and maintained. All equipment is certified, besides nucleic acid automated extractor.

The laboratory also reported unavailable equipment: - Plexiglas screen - Biosafety Cabinet class II

Facilities

The general condition of the lab needs improvements. Windows (wooden) and doors, as well as walls, floors and roofs are at medium conditions. There are no benches. During assessment was also reported the absence of heating, air conditioner and ventilation. It is cold in premises in winter. Lighting and waste disposal equipment (autoclaves) are in good condition. The lab sometimes faces electricity and water interruptions. The generator is absent. Key equipment is partially protected by UPS. The laboratory noted having 275 m2 for its activities. It was reported that it is not enough to perform nucleic acids extraction and RT-PCR with available space. The area needs restructuring for more efficient use of it. Master-mixing is conducted in UV box located in the same room with adding of nucleic acids in the separate UV box.

Human resources

13 people composes laboratory team: 3 senior staff representatives, 7 laboratory technologists and 3 laboratory assistants. The lab reported that staff number is not adequate to undertake required work, but there is no surge plan. 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 position of quality manager is filled, while the position of biosafety officer is absent and not filled. Personnel of the lab received training on quality management, while training on biosafety is needed (in the part of conducting of risk assessment). Staff is also trained on molecular biology and serology assay optimization. Further training in PCR, optimization, and understanding troubleshooting will be helpful.

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. Rooms have different sinks for handwashing only (one per unit). BSC is absent in the lab. 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 not correctly managed. Lab coats and laboratory linens are washed at the lab. There are locks on the freezers with primary specimens and aliquots stored.

PPE are available in enough quantities for the work load and number of laboratory personnel. Staff adheres 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. The laboratory is aware of designated national reference laboratories for SARS-CoV-2. The lab has defined responsibilities in national preparedness and response to public health emergencies like COVID-19 pandemic. The lab receives specimens from the files during investigation of public health events or surveys. It also gives advice on specimen collection and transport practices from the field. The lab has a stock of emergency laboratory sampling kits (PPE, sample collection material, transport media, sample transport packaging).

The lab refers specimens to Donetsk Oblast Laboratory Center for public health purposes (e.g. routine surveillance, outbreak investigation). The lab does not receive clinical specimens from local laboratories for confirmation and other tests. 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. 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 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 required to be created and adapted. Appropriate PPE for the handling and testing of specimens for SARS-CoV-2 are available. Personnel is trained in running SARS-CoV-2 testing

with the help of such platforms as RT-PCR, Bio-Rad CFX96 Dx. The lab was not assessed for competency before testing for SARS-CoV-2. 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 which is not always the case. The lab participates in EQA for the SARS-CoV- 2 test. The system to record and assess EQA results is present.

Assessed laboratory may ask referent lab for referring specimens for confirmation of the results, but there is no guarantee that referent lab will pick up the phone and accept specimens. Personnel is not trained in troubleshooting SARS-CoV-2 PCR results and a change in assay performance.

V. Conclusions/Recommendations

The laboratory might implement: 1. Risk assessment is required to implement. 2. Biosafety manual needs to be updated and adapted with the actual laboratory procedures. 3. LIMS is recommended to set-up. 4. 2 BSCs are recommended to have as soon as possible. 5. PCR lab needs to review its workflow in order to make changes to avoid contaminations 6. Biosafety position is recommended to create and fill. Next steps might be done by partners/WHO: 1. Trainings on transportation of infectious substances, validation procedures, quality assurance, biosafety needs to be conducted. 2. Support in purchasing Laboratory information system and BSC.