Yemen COVID19 Laboratory Testing Strategy Final _ 6.7.2020 _ Laboratory Testing Strategy for COVID-19, YEMEN

Contents

Purpose of this strategy...... 3

Who gets tested...... 7

Laboratory testing procedures for covid-19...... 8

Laboratory indicators data and surveillance...... 1 0

Annex 1: COVID-19 Laboratory requisition form...... 1 1

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Purpose of this strategy

The objective of COVID-19 testing is to identify Human Resources individuals with COVID-19 infec-tion, isolate and manage laboratory con-firmed cases, and The table 1 shows the total number of undertake rapid con-tact tracing for exposed in- laboratory staff (Laboratory techni-cians/ dividuals to reduce the transmission and spread. technologist) working in the each of the The strategy will allow those having a higher risk laboratories and the number that has been of poorer outcomes from COVID-19 infection trained so far. be rapidly identified and prioritized for accessing health care services. Laboratory data will also be used to supplement epidemiological da-ta for a comprehensive COVID-19 surveil-lance system. This strategy should be read together with other detailed WHO technical guidance on COVID-19 labora-tory and diagnosis . Case Definition: COVID-19 case defini-tions are as per WHO guidelines and are also outlined in the Yemen Covid-19 Surveillance Strategy.

Situation overview

Six laboratory facilities in Yemen are cur-rently able to test for COVID-19, four are in the south and two are in the north. By end June 2020 the laboratories in the north were fully functional and had re-ceived supplies to conduct up to 40,000 tests. In the South, 10,500 PCR diagnos- tic kits have been provided by WHO, however other necessary supplies like RNA isolation kit and PCR plastics (tubes/caps) provided so far are only enough to conduct 4500 tests. More PCR diagnostic kits and essential consuma-bles are expected to be delivered in the coming weeks.

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Table 1: Trained laboratory staff capacity in Yemen

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PCR Machines

Except Sanaa CPHL, all other testing laborato- tions in the South and North have ries have one PCR thermocycler for performing two different approaches in terms the molecular detection of COVID-19. Sanaa of expanding access to laboratory CPHL have two functional PCR thermocyclers. testing for COVID-19. While the With one PCR machine, a single laboratory can Southern part of the Yemen adopted perform two testing runs per day with each run a decentralized testing strategy analyzing at least 90 samples from suspected where testing is availed in every cases. Hence, in total a single laboratory with all governorates, the MOPHP in North the necessary requirements can perform testing favours centralized testing for reason for 180 samples a day. The six testing laboratories of having better control on quality in Yemen have capacity to perform 1080 samples procedures as only the Sanaa Central every day within normal working hours without labs have trained laboratory person- overwhelming the laboratory system. Currently, nel who are proficient in performing the combined throughput of the 6 testing CPHLs real time RT-PCR assays. Emphasis average about 200 samples a day which is below will therefore be made regarding the available capacity. putting in place a robust laboratory An extra 11 PCR machines are expected into the sample transport system, and results country courtesy of HSA donation (5 machines), feedback system to cover all gover- and WHO procurement (6 machines). A new norates. The envisaged mechanism machine for Hodeidah Central Public Health can be supported ether by partners Lab (CPHL) has been delivered and is ready for or by revitalized polio surveillance installation. These new PCR machines provided structures. together with all the necessary accessories re- quired for a complete PCR test will be essential in expanding access to COVID-19 testing and in improving the testing output of the existing laboratories. All laboratories currently perform manual ex- traction of RNA using commercial kits. There is no laboratory testing COVID-19 with automated RNA extraction machine at the moment. This factor needs to be considered when planning ex- pansion of testing output as the RNA extraction step is a labour-intensive step especially when dealing with large number samples. It is important to note that the two administra-

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Enhancing or improving testing capacity: Some of the activities planned to enhance testing capacity are as follows (details in Annex 3);

• Establish 3 more PCR testing laboratories in Ibb, Hodeida, Saada.

• Deploy point of care PCR Diagnostic machines (GeneXpert) in Socotra, Al-Maharah, Marib

• Ensure availability of testing kits, routine supplies, and consumables.

• Train more laboratory staff • Ensure compliance to SOPs and testing algorithms through frequent supportive supervision. The map below shows the existing and planned PCR labs as well as locations of the point of care diag- nostic PCRs (GeneXpert) in the country.

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Who gets tested:

WHO recommends that all suspected or probable cases who meet the standard case definition be tested for COVID-19. This strategy therefore recommends the following individuals to get tested: • All suspected cases as per established COVID-19 suspect case definition • All probable cases as per established COVIFD-19 probable case definition • All SARI/Pneumonia cases (requiring admission) • Testing of contacts (in home or facility quarantine) who develop symptoms • Close household caregivers (even if asymptomatic) of confirmed pneumonia/COVID-19 • Exposed health care workers or Laboratory workers who has handled a covid-19 patients or laboratory specimens without PPE

High priority for testing It is anticipated that testing capacity will remain constrained for a consider- able length of time due to shortage of test kits or other operational issues; therefore, prioritization of testing will be conducted due to limitations in testing, and also in view of increasing community transmission of COV- ID-19. Groups or individuals prioritized highly for testing are as follows:

1. Suspect or probable cases amongst vulnerable populations, detainees, refugees, IDPs, migrants, residences

2. SARI/pneumonia patients admitted in hospital

3. Health care workers, RRTs, contact tracers, community volunteers, po- tentially exposed, both in health facilities and at community levels, and who develop symptoms

4. Mothers seeking urgent maternity care, emergency cases, children under five with wasting, with symptoms when detected at triage at ‘non-COVID’ health facilities.

5. Travellers at POEs (air and land border crossings) who develop symp- toms

6. Close household caregivers of confirmed cases, and who develop symp- toms

7. Individuals at risk of developing severe disease due to age, presence of comorbidities, or other risk factors. 7 Page Final _ 6.7.2020 _ Laboratory Testing Strategy for COVID-19, YEMEN

Laboratory testing procedures for covid-19

a) Testing algorithm b) Biosafety Laboratories undertaking testing for COVID-19 Testing for COVID-19 virus is a two-step process, virus should adhere strictly to appropriate biosafe- involving first a screening assay for both SARS ty practices. This include conducting risk assess- virus and COVID-19 virus, and secondly, a con- ment before handling clinical samples, identifying firmatory assay for COVID-19 virus only; procedures that are likely to produce risks and putting in place measures to eliminate or reduce 1. Screening with E gene assay to detect both such risks. Diagnosis of COVID-19 by a Real Time SARS virus, MERSCOC and SARS-COV2 PCR test requires (Biosafety Level 2) laboratory. All laboratories conducting tests for COVID-19 2. Confirmation with RdRP gene assay to detect in Yemen are BSL 2 and each one of them has at SARS-COV2. least one class 2 biosafety cabinet where sampling processing is conducted. Laboratory staff have also The above procedure was applied in Yemen in been trained on bio-safety due sample processing the beginning of the outbreak, whereby samples and were provided with all updated guidelines on positive on the screening assay were then ana- biosafety as regards to COVID-19 samples han- lysed with a confirmatory assay that is specific dling from WHO. to SARS-COV2. However, it became apparent that conducting the screening and the confirma- tory assays in an area with high positivity rates c) Sample collection was both labour and resources (tubes, tips, caps, At minimum, respiratory material should be col- gloves) intensive. As results, laboratory test- lected with strict adherence to infection preven- ing strategy was reviewed to perform only the tion and control procedures as follows: screening assay, which is more sensitive assay. Samples are now analysed using only one assay • Upper respiratory specimens: nasopharyngeal and with final results of a patient are based on the and oropharyngeal swab or wash in ambulatory outcome of the screening assay. This simplified patients, and/or testing strategy is widely practiced by countries in the regions and has been shown to be offer a • Lower respiratory specimens: sputum (if pro- similar diagnostic accuracy when compared with duced) and/or endotracheal aspirate or bron- two-step diagnostic assays. In the meantime, pro- choalveolar lavage in patients with more severe curement has been initiated at the country level respiratory disease. for multiplex assays that combine the detection of 2-3 genes in a single reaction tubes hence saving All specimens delivered to the testing laboratory on time and consumables and delivery of these should be accompanied by a completed labora- kits is expected in the coming weeks. tory test request form (Annex 1)

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EQAP and Training d) Sample packaging and transport It is required that all COVID-19 laborato- ries are to participate in WHO SARS-CoV-2 Specimens for virus detection should reach External Quality Assurance Program (EQAP). the laboratory as soon as possible after collec- Currently two laboratories – Sanaa and Aden tion. Correct handling of specimens during are participating in WHO SARS-CoV-2 transportation is essential, ensuring that EQAP EQAP organized by Centre for Health collected swabs are packaged properly using Protection (CHP) of the Department of the triple package systems and delivered to Health, Hong Kong. EQAP samples have been the testing laboratory. Specimens that can be received in Yemen and the two participating delivered promptly to the laboratory can be labs will submit their analysis to organizers. stored and shipped at 2-8°C. When there is likely to be a delay in specimens reaching the A total of 28 laboratory technicians have laboratory, the use of viral transport medium been trained on PCR technique and biosafety is strongly recommended. Once, in the labora- as pertains to handling specimen from sus- tory, lab staff will document the patient details pected COVID-19 patient. Second round of and give the sample a unique identification training is planned to be conducted in the number. The samples are analyzed according third quarter of 2020. to the existing SOPs and results are released in the same day. Training on sample collection, packaging and To reach governorates located outside testing transport will also be provided to staff at tri- laboratories, plans are on-going to procure age EHS (NON-COVID HFs), RRTs, and to courier services to enable sample referral all other HCWs who will be involved in the system. It is anticipated that samples from collection and transport of samples. suspected cases in a defined district/governo- rate will be collected through the RRT system, Private and other Laboratories pre-stationed at a central location (usually governorate hospital lab), and be picked-up Testing facilities run by partners and NGO, as by the appointed courier service provider. well as private for-profit laboratories will be The frequency of collection will depend on required to align their testing kits and proce- the sample volume but a daily collection dures according to WHO/MOH/CPHL guid- and delivery to one of the CPHL testing site ance, participate in EQAP and training, and within a period of not more than 72 hours they should also regularly share COVID-19 from time of collection is expected. test data with MOH.

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Laboratory indicators data and surveillance

Daily indicators Weekly indicators

All laboratories with the capacity to test for SARS- To assess access to testing facilities and the ad- CoV-22 should report daily: equacy of testing per region, the following indica- • Total persons tested for SARS-CoV-2 tors should be measured on weekly basis. • Total number of persons testing positive for 1. Number of COVID-19 PCR tests conducted SARS-CoV-2 (and any testing inconclusive) per 1000 people for every governorate • Total number of tests performed for SARS- CoV-2 per type of testing method. 2. COVID-19 PCR test Percent Positivity (total positive/total test) for every governorate Hospital laboratories should also report to the central level, on a regular basis (e.g. weekly), the complete information on tested patients (e.g. age, sex/gender, residence, date of symptom onset, and any other data collected) to permit more in-depth analysis of testing patterns.

A sample of laboratory test request form is at- tached for reference (Annex 1). Arabic version is available. Lab line list - a uniform lab line list has been developed and a sample format is attached (Annex 2). Most labs use this format except Mu- kalla CPHL.

Laboratory data will be integrated with national COVID-19 epi data for surveillance purposes. Lab Line lists will be submitted daily to surveil- lance and information management teams at WHO and MOH who will use the same to update their dashboards and produce other information products, and calculate required indices such as COVID-19 population testing rates per Governo- rate, and test positivity rates (TPR) per Governo- rate.

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Annex 1: COVID-19 Laboratory requisition form

Annex 1: COVID-19 Laboratory requisition form COVID-19 Surveillance Unique Sample Lab Laboratory Requisition and Report form ID no.

Ministry of Population and Public Health National Central Public Health Laboratory – Aden Lab Request and Reporting Form Date of collection: ______Date of disease onset: ______Patient information Name: Age: Sex:

Unique Case ID no.: Phone Number:

Type of sample: tick where appropriate Reason for testing (tick where appropriate)  Oral/Nasopharyngeal swab  Travel to country with confirmed cases  Sputum  Contact with confirmed/probable case  Bronchoalveolar lavage  Has typical clinical symptoms  Tracheal Aspirate  Others: ______

Demographic information Governorate: District:

Location: Village:

Clinical Symptoms (Tick where appropriate)  Fever  Cough  Respiratory Distress  Sore throat  Other symptoms, specify: ______

Laboratory Report Realtime PCR Results Target gene – SARS- CoV2 (to be reported as Negative or Positive) 1. Screening Test – E-Gene Lot Number: ______

2. Confirmatory tests RdRP/orf1b Lot Number: ______

3. Other, specify: ______Lot Number: ______

Conclusion:

Positive results: indicates that an individual is infected with SARS-COV2 (causative agent for COVID-19) Negative result: may mean the patient is not infected with the virus causing COVID-19, or that the patient has been tested too early, and may test positive later. In that case, the patient may need to be re-tested if the patient continues to show symptoms or deteriorates clinically. Negative results should also be based on eval- uation of date of disease onset, and consideration of optimal sample type. Name of laboratory technologist: ______Date: ______Signature:

Report reviewed by: ______Date: ______Signature:

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Activities Primary Co- Source Target Estimated Main Objective Responsible responsible of Governorates funds (USD) Officer staff funding A Aseemah, Aden, Provide training for laboratory staff on technical procedures, biosafety, good lab Taiz, Hodeida, Dr. Saeed Al- Ismail M WB practices (GLP), and reporting techniques for all testing laboratories. Hadramaut, Ibb, Shaibani Bashir Saada 48,000

Dr. Saeed Al- Ismail M All governorates WB Procurement of additional NPS swabs/VTMs, PCR testing kits, RNA isolation kits, Shaibani Bashir tubes/tips and routine consumables required to perform a PCR tests. 1.100,000 Procurement of additional lab equipments to expand testing for selected Dr. Saeed Al- Ismail M All governorates WB laboratories Shaibani Bashir 850,000 A Aseemah, Aden, Development guidelines and SOPs for collecting clinical samples and Taiz, Hodeida, Dr. Saeed Al- Ismail M Ensure that national laboratories performing testing for suspected cases. Provide arabic translated versions to WB Hadramaut, Ibb, Shaibani Bashir identified for providing testing for COVID- all testing laboratories Saada 50,000 19 have the appropriate capacity and For governorates without lab capacity for testing COVID-19, Support the readiness to provide timely and quality Dr. Saeed Al- Ismail M transportation of samples from THE health facilities to the nearest testing All governorates WB laboratory reports. Shaibani Bashir laboratories. 100,000 A Aseemah, Aden, Support all testing laboratories to participate in external quality assessment Taiz, Hodeida, Dr. Saeed Al- Ismail M WB schemes organized at the regional level (EMRO). Hadramaut, Ibb, Shaibani Bashir Saada 30,000 A Aseemah, Aden, Provide quarterly supportive supervision and facility assessment to assess Taiz, Hodeida, Dr. Saeed Al- Ismail M WB compliance to SOPs, biosafety guidelines, GLPs and Hadramaut, Ibb, Shaibani Bashir Saada 25,000

Organize targeted testing of populations through campaign of mass testing for Dr. Saeed Al- Ismail M All governorates COVID-19 Shaibani Bashir 300,000

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