Microbiology Laboratory, Kramatorsk City Branch of Donetsk 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 2 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 3 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 4 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 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 5 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. 6 Specimen collection, handling and transport Specific collection procedures used for specimens are partially documented. Internal system includes minimum patient identification