MediLabSecure: A One Health Network Facing the COVID-19 Pandemic DVM

Introduction

In December 2019, the first official human case of SARS-CoV-2 was reported in China,^1,2 starting the biggest 21st century pandemic so far. Rapidly, Chinese scientists identified and characterized this new coronavirus and shared openly its sequence, ³ allowing scientists worldwide to design molecular (reverse transcription quantitative polymerase chain reaction [RT-qPCR]) tools to detect potential human cases in travelers matching the clinical case definition. This international cooperation was essential for the detection of first cases, and, potentially, helped countries better manage the spread of the disease within their own borders.

This pandemic was predicted by many international experts after the emergence of severe acute respiratory syndrome (SARS; 2002), Type A/H1N1 influenza (2009), Middle East respiratory syndrome (MERS; 2012), Ebola in West Africa (2013), or Zika (2015). These warnings had been considered seriously by the scientific community and international health organizations. As an example, the World Health Organization (WHO) regularly conducted simulation exercises based on scenarios of viral outbreaks including influenza or coronaviruses. ⁴ Many countries and organizations have been working on preparedness to face an emergence or reemergence of human infectious diseases. In this respect, since 2014 the European Union supported the MediLabSecure project, ⁵ an international network that aimed to enhance preparedness, prevention, and control of relevant emerging zoonotic viruses in Mediterranean, Black Sea, and Sahel countries with a special focus on arboviral infections and other emerging viruses threatening the region.

MediLabSecure, and its following project OneHealthSecure, promoted the One Health approach and consisted of reference laboratories for human and animal virology, medical entomology, and key national institutions for public and animal health in each of the 22 non-EU countries involved (Figure 1). It is a central source for awareness, risk assessment, surveillance, monitoring, and control of relevant emerging diseases. At the laboratory level, MediLabSecure notably implemented and/or improved emerging pathogen detection capacities, with a particular emphasis on biosafety and biosecurity processes.^6,7 The project put notable effort into the implementation of quality and biosafety procedures, diagnostic tools for emerging viruses,^6-9 and advocacy for the One Health approach.^10,11 Although the project mainly focuses on arboviruses, ¹² other emerging viruses threatening the region have been targeted in the past. This was the case for the MERS-CoV, a coronavirus that has been menacing Middle East and Maghreb countries since 2012. In 2018, 83% (n=15) of the 18 laboratories from the human virology network reported capacities to identify the MERS-CoV in biological samples.

OPEN IN VIEWER

Figure 1.

Human (top) and animal (bottom) virology networks of MediLabSecure. Countries, institutions, and laboratories are indicated.

Numerous international networks, scientific projects, institutions, and organizations participated in international efforts to respond to the COVID-19 crisis. Among those, we describe the actions set up by the MediLabSecure network in management and control of the COVID-19 pandemic in its geographic area. In early 2020, when COVID-19 threatened the region, the MediLabSecure network established a rapid communication online group for members to answer questions and support each other in the implementation of capacity diagnostic tools and decision algorithms. This objective was achieved through the sharing of information, molecular protocols, positive controls, and diagnostic reagents, facilitating the implementation of working detection tools in the region. Then, the project supported the sequencing of the first strains and variants detected through the import of positive patient samples and direct NGS sequencing of the virus by the coordinator laboratories. Following the positive impact of this action, the project organized the training for the sequencing and characterization of the SARS-CoV-2, either by sponsoring the participation of scientists in other initiatives’ trainings or by directly training involved laboratories. During the first months of the pandemic, MediLabSecure organized an evaluation of diagnosis quality and accuracy through external quality assessment (EQA). Overall, the existence of the MediLabSecure network, a well-established, long-lasting collaborative network of experts throughout the Mediterranean, Black Sea, and Sahel regions, was instrumental in the rapid response to the crisis in the region.

Diagnostic Capacities of Human and Animal Virological Laboratories of the Network

Beneficiary laboratories for the human and animal virology networks are recognized as national or international reference laboratories for viral identification and diagnostics (Figure 1). Each network is coordinated by a leading laboratory belonging to the project consortium and using well-established communication tools such as instant messaging, group emails, newsletters, or the project webpage. In the context of COVID-19 pandemic, the involvement of network laboratories in diagnosis was evaluated through 2 online surveys in May 2020 and April 2021 for animal virology laboratories, and 1 survey in 2021 for human virology laboratories. In May 2020, 21 of the 22 laboratories responded to the surveys, and 20 responded from animal virology and 21 from human virology in April 2021. All 21 laboratories from the human virology network were involved in the COVID-19 diagnostics, 14 of them starting as early as January or February 2020 and 18 of them in March (Figure 2A). Most (n=18) of the 21 laboratories were firstline diagnostic laboratories meaning that they were national reference laboratory or equivalent, for SARS-CoV-2 identification. Additionally, to face the overwhelming number of diagnostic requests, some countries required support from veterinary laboratories. Within the 20 animal virology network laboratories that responded to the survey, 8 were involved during the first wave in the SARS-CoV-2 diagnostic, supporting human diagnostics. By 2021, up to 12 laboratories were involved in diagnosis for both humans and animals (for companion pets and zoo animals). However, at first, very few laboratories were prepared and equipped to identify an entirely new emergent virus.

OPEN IN VIEWER

Figure 2.

Questionnaire sent to the human virology network of MediLabSecure from December 2020 to September 2022. Almost all (n=21, 95%) of the laboratories answered the surveys.

Diagnostic Tools and Technical Implementation

Following the first alert from WHO in early 2020 regarding the emergence of SARS-CoV-2, ² specialized public health and virology networks communicated to alert key actors in the surveillance systems in each country. In the Mediterranean region, EVD-Labnet, EMERGE, EMPHNET,^13-15 and MediLabSecure among others, as well as WHO regional offices relayed confirmed and relevant information to their networks. Though it was initially advised to identify the new coronavirus using a pancoronavirus RT-qPCR, the release of the full sequence of the SARS-CoV-2 on January 12, 2020, ³ made it possible to design specific RT-qPCR protocols. Among the first protocols published, the coordinators of MediLabSecure shared with the animal and human virology networks 1 proposed by Peiris et al ¹⁶ at the HKU Medical University in Hong Kong and 1 proposed by Corman et al ¹⁷ from Charité hospital in Berlin, along with the WHO Laboratory Biosafety Guidance Related to Coronavirus Disease (COVID-19), Interim Guidance ¹⁸ for the safe handling of human samples for 2019-nCoV (later SARS-CoV-2), followed by the updated versions. For all communication between sectors, the animal and human virology networks used each other’s long-term established communication tools to facilitate interactions. Additionally, the coordinators of the animal virology network of MediLabSecure participated in the production of the World Organisation for Animal Health guidelines for the testing of human diagnostic specimens in veterinary laboratories ¹⁹ and shared them with the concerned beneficiary laboratories to promote efficient intersectoral collaboration at the laboratory level during the crisis.

The first challenge for all laboratories at this initial point was to obtain reagents and generate positive controls for these protocols, as the virus had not yet been isolated in most countries. The public and private sectors were overwhelmed with requests and faced difficulties responding in a timely manner. MediLabSecure organized an online survey to evaluate the need within the network of 22 human virology laboratories and obtained 16 responses requesting support for positive controls and reagents in less than 24 hours. The coordinators of the human virology network of MediLabSecure produced positive controls for the Corman et al ²⁰ protocol using a strain of SARS-CoV-1 isolated in Germany in 2003 (Frankfurt-1) and shared it by the end of January 2020 with requesting laboratories. In the meantime, reagents were purchased from TIB Molbiol ²¹ consisting of primers, probes, and positive controls (WUHAN-CoV kit primers and probes 2020; positive controls: 30-7437-71 Wuhan E-gene RNA; 30-7437-71 Wuhan E-gene RNA; 30-7440-71 Wuhan RdRP RNA), according to Corman et al protocol, and dispatched to all requesting partners, including laboratories from the animal virology sector, during the first 2 weeks of February 2020. An online hotline was set up within the human virology network to discuss technical and scientific issues and to support the implementation of diagnostic tools. It was active for the duration of the pandemic and was deemed a very useful resource for all participants. Following this implementation step, MediLabSecure dispatched additional kits over the following months when some laboratories were facing supply disruption due to the discontinued international trade and travel. Overall, during the first 6 months of the pandemic, the MediLabSecure project organized 34 international shipments to partners in 21 countries (16 from the network and 5 from West and Central Africa) corresponding to about 23,000 RT-qPCR reactions.

As demonstrated by the numerous SARS-CoV-2 outbreaks in mink farms in Europe and North America, ²² this virus was able to jump from humans to certain animals and jump back again to humans. During the pandemic, it quickly became necessary to implement viral surveillance in animals, especially mustelids in fur farms, pets in affected households and wildlife in zoos and in the field. A technical document compiling all available information about SARS-CoV-2 in animals was produced by the coordinators of the animal virology network of MediLabSecure and shared with all laboratories. The first version was circulated in May 2020; it was updated on 4 occasions during the following year ²³ to include new information about species susceptibility based on natural and experimental infections, countries affected, laboratory diagnosis in animal samples, and so on. In February 2021, a dedicated workshop with international experts was organized online to offer an update on the epidemiological situation in domestic and wild animals and to share information about diagnostic methods in different species of animals. This event gathered 55 participants from animal virology, human virology, public health, entomology, and veterinary services.

To demonstrate the importance of the MediLabSecure network in the region and this initial support, 20 of the 21 human virology laboratories were involved in the identification of the first cases in their countries (Figure 2B). At least 15 laboratories (71.5% of the network, 94% of the partners requesting kits) declared that the reagents sent by the project were essential for setting up these techniques in their laboratory and/or in the identification of their very first cases (Figure 2C). Among these laboratories, colleagues at the Rafik Hariri hospital in Beirut, Lebanon, received patients for suspected COVID-19 infection as early as January 2020, before they received the reagents sent by the project. Considering the time necessary to ship the diagnostic kits and implement the new technique, they decided to send suspected human samples to the coordinator laboratory in Paris. Processed immediately at reception, diagnostic results were available within a couple of days. At the same time, the Lebanese colleagues received the diagnostic kits and implemented the technique. The following weeks, they were capable of identifying the first positive case in Lebanon. ²⁴

Additionally, most of the 21 laboratories were involved in other activities related to the response to the pandemic (Figure 2D): over 76% (n=16) of the laboratories were regular scientific advisors for their government, and about 81% (n=17) of the laboratories were involved in advising and training other laboratories in the country. Additionally, about half of the network was also involved in research projects on the virus and/or in the development or evaluation of diagnostic tools.

Organization of External Quality Assessment

During the first pandemic wave, a range of commercial diagnostic kits and in-house protocols were shared regardless of their level of performance (sensitivity and/or specificity). Even using the same protocol, each laboratory was using different reagents, which likely affected the quality of the results. As a common tool to control and guarantee the efficiency and quality of the diagnostic techniques, EQA was especially important for SARS-CoV-2 molecular detection since laboratories were implementing the new diagnostic techniques using protocols and reagents that might not be optimal. Quality Control for Molecular Diagnostics (QCMD), ²⁵ an independent international EQA provider focused on molecular detection of infectious diseases, proposed an EQA to evaluate the quality of diagnostics within the COVID-19 outbreak preparedness phase as early as March 2020. ²⁶ MediLabSecure offered to support all beneficiary laboratories involved in SARS-CoV-2 diagnostics with their participation in this EQA scheme. Thirteen laboratories from the human virology and 10 from the animal virology networks registered to participate.

Unfortunately, the international logistics situation at this time was complex, the EQA panels were not delivered until summer 2020. Out of 23 laboratories, 18 received the samples and 12 answered in time (75% success in the identification of the core samples). Six laboratories were overwhelmed and could not send their results on time. Five laboratories, mainly in Africa, could not receive the panels due to international shipping issues (no international travel or no cold chain for shipment).

The QCMD EQA scheme for SARS-CoV-2 (QCMD 2020 Coronavirus Outbreak Preparedness EQA Pilot Study, CVOP20 ²⁶ ) consisted of a panel of 8 samples (Table): 5 positive samples containing serial 10-fold dilutions of inactivated SARS-CoV-2; 2 “specificity” controls with other cell culture-derived human coronaviruses (HCoV-OC43 and NL63) considered “educational,” meaning that they are not necessary to succeed in the program since some laboratories might also use pancoronavirus protocols; and finally 1 sample containing a transport medium only (true negative control). Seven laboratories declared using an in-house protocol (including the 1 shared by the project) and 5 declared using a commercial kit (DaAn Gene, Genesig (x2), Bioeksen or Shanghai ZJ Bio-tech). Six of the 7 laboratories using an in-house protocol succeeded in the identification of all samples from the EQA scheme. The seventh failed to identify the least concentrated sample, showing a defect in sensitivity in their technique. Two of the 5 laboratories using commercial kits succeeded in the identification of all samples, and 1 failed to identify as negative the 2 “educational samples” (specificity issues) but still passed the scheme. Two laboratories using a commercial kit failed to identify 2 or more of the positive samples, failing the scheme. The results for all the laboratories are available in the Table. Interestingly, this EQA scheme within the MediLabSecure group pointed out issues with the handling of some commercial kits available at the beginning of the pandemic. Whether these issues were due to defects inherent to the kits, their shipment or storage, or the manipulation by the staff remains unknown. Moreover, in-house protocols and reagents used demonstrated more reliability in this specific situation.

OPEN IN VIEWER

Table.

Results from QCMD 2020 Coronavirus Outbreak Preparedness EQA Pilot Study, CVOP20

Lab No.	Sample No, Content, and Viral RNA Concentration								Method	Result(n=9)
	#1SARS-CoV-2>10^4 copies/mL a Core	#2HCoV-NL63 b >10^5 copies/mL a Educ	#3SARS-CoV-2>10^3 copies/mL a Core	#4HCoV-OC43 b >10^4 copies/mL a Educ	#5True Neg.∼Core	#6SARS-CoV-2>10^4 copies/mL a Core	#7SARS-CoV-2>10^5 copies/mL a Core	#8SARS-CoV-2>10^2 copies/mL a Core
1	+	-	+	-	-	+	+	+	In-house	Succeed
2	FN	-	+	-	-	+	+	FN	Commercial	Failed
3	FN	FP	+	-	FP	+	FN	FN	Commercial	Failed
4	+	-	+	-	-	+	+	FN	In-house	Failed
5	+	-	+	-	-	+	+	+	In-house	Succeed
6	+	-	+	-	-	+	+	+	In-house	Succeed
7	+	FP	+	FP	-	+	+	+	Commercial	Succeed
8	+	-	+	-	-	+	+	+	Commercial	Succeed
9	+	-	+	-	-	+	+	+	Commercial	Succeed
10	+	-	+	-	-	+	+	+	In-house	Succeed
11 c	+	-	+	-	-	+	+	+	In-house	Succeed
12 c	+	-	+	-	-	+	+	+	In-house	Succeed
Success d	83%	83%	100%	92%	92%	100%	92%	75%		75%

a

Viral RNA concentration: Values are indicative and provided for reference only and have been established to support the consistency and traceability of the EQA materials as well as comparison of results across participating laboratories. Real values were obtained using a digital PCR assay (modified from Corman et al ¹⁷ ). Samples #7, #1, #3 and #8 are in a calibrated dilution series. Sample #6 is a duplicate sample of #1.

b

Sample Status: Samples #2 (HCoV-NL63) and #4 (HCoV-OC43) are defined as “Educational (Educ)” specificity samples and were expected to be reported as SARS-CoV-2 negative. Participants were not expected to report on the identity of the common human coronaviruses HCoV-NL63 or HCoV-OC43. Their correct identification was not necessary to succeed in the scheme. Participating laboratories were expected to report Core (Core) proficiency samples (here: all SARS-CoV-2-positive samples and the negative control) correctly within the EQA scheme.

c

Laboratories #11 and #12 participated in a second EQA scheme (QCMD 2020 SARS-CoV-2 EQA Program—Challenge S, SCV_20S). The structure of the scheme was equivalent with notable difference HCoV-229 replacing HCoV-NL63.

d

Success: Percentage of datasets reporting the correct qualitative result for each panel member, percentage correct (overall), and total number of laboratories for all core samples.

Abbreviations: CVOP, coronavirus outbreak preparedness; EQA, external quality assessment; FN, false negative; FP, false positive; QCMD, Quality Control for Molecular Diagnostics; PCR, polymerase chain reaction.

Sequencing and Trainings

Sequencing has been the key technological approach of global public health responses, making it possible, for example, to track the pandemic coronavirus, study clusters, determine entry points within countries, and provide information on the viral evolution, particularly the emergence of the first variants at the end of 2020. At first, the human virology coordinator laboratory of MediLabSecure assisted requesting beneficiaries by directly sequencing their first positive samples and, later, their first suspected variants. Their data helped identify viral entry points in Tunisia and Lebanon.^27,28 During the pandemic, numerous laboratories invested in sequencers and reagents to implement this new capacity locally. MediLabSecure offered to train all equipped laboratories to sequence the emergent virus on their own. Numerous partners from other institutions and organizations, such as the Wellcome Connecting Science, WHO, Africa Centres for Disease Control and Prevention, and others, worked at implementing trainings on sequencing and data analyses of SARS-CoV-2. The project advertised these training when informed and facilitated the participation of members of the network when possible. Then, MediLabSecure updated and shared with all beneficiary laboratories the standard operative procedures for whole genome sequencing using the traditional Sanger technology ²⁹ or the nanopore portable MinION device (Oxford Nanopore Technologies, using the up-to-date version of the ARTIC protocol ³⁰ ). The project organized 2 hands-on workshops on MinION nanopore sequencing of SARS-CoV-2, the first in 2021 in Algiers for 10 trainees coming from 5 countries of the network (Algeria, Niger, Republic of North Macedonia, Tunisia, and Turkey) and the second in Morocco in 2022 for 5 trainees from 2 additional countries (Mauritania and Morocco). After these trainings, all 7 countries demonstrated an independent capacity to sequence biological samples, analyze the data, identify the variants, and share the obtained genomes on the public online databases. The impact of these capacity building activities can be illustrated by the Tunisian experience. During the first wave of COVID-19 in Tunisia, the project supported the Institut Pasteur de Tunis, beneficiary laboratory of the project in Tunisia, in the sequencing of the first positive SARS-CoV-2 samples of the country. ²⁷ Following this positive experience, the institute invested in NGS sequencers and scientists were trained during the workshop organized in Algiers in 2021. The laboratory sequenced SARS-CoV-2 and other viruses and shared 870 sequences of SARS-CoV-2 on public online databases in 2022.

Conclusion

The MediLabSecure project aimed at preventing emerging infectious diseases through multiple and complementary actions in its geographical area. The project worked mainly to prepare beneficiary countries to face public health crises through capacity building and technical training. However, on multiple occasions, during local or regional outbreaks, the project had to adapt from preparation to response and support. The COVID-19 outbreak has been the most critical example of the positive impact of the project in times of emergencies.

The aim of this case study is to advocate the importance of One Health initiatives similar to MediLabSecure in the region and worldwide. International public health networks and projects, such as MediLabSecure, play a critical role in ensuring the efficiency and resilience of our systems and the sustainability of the lessons learned from each crisis. The rapid and efficient international cooperation promoted within these networks, and between the different sectors following the One Health approach, was critical for many countries and for the entire region during the first wave of the pandemic—at a time when many politicians were not yet concerned enough or were too overwhelmed trying to cope with the situation. From our point of view, the complementarity, cooperation, and interoperability of the multiple actions set up by numerous international partners within the project during the pandemic was efficient and supportive. However, we feel that, in general, the opportunity was missed. This was likely because of the regionality of the networks, siloing of work and/or funding, lack of communication, lack of global coordination, and perceived level of emergency of the situation.

Looking at One Health trans-sectoral coordination, the project used well-established communication tools rather than attempting to create new ones and wasting time and money. All the sectors involved received communications through their usual trustworthy media. The status of the project participants’ sentinel laboratories and their national and international visibility with emerging viruses, were among the reasons for MediLabSecure’s success during the COVID-19 pandemic. All laboratories were equipped and trained for handling and performing viral detection in biological samples and simply needed tools and standard operative procedures to adapt their processes to this emergent virus. All 21 human virology laboratories and about 12 animal virology laboratories were involved in the diagnostics of COVID-19, and 20 of the human virology laboratories were involved in the identification of the very first cases in their countries. It is noteworthy that, in addition to MediLabSecure support, 5 laboratories also received reagents from other networks or from WHO, highlighting once again the importance, interoperability, and efficiency of international networks. Additionally, most laboratories were involved in further activities related to the response to the pandemic, such as scientific advising, training, research projects, and the development of diagnostic tools. The added value of the One Health component of MediLabSecure was also highlighted during the pandemic, with veterinary and public health laboratories benefiting from each other’s expertise. The MediLabSecure approach, which combines the sharing of information and protocols, support with reagents, technical training of staff, troubleshooting, and organization of EQAs, proved to be highly efficient during this crisis. Additionally, the COVID-19 pandemic was the opportunity for important progress in capacity building and the development of diagnostic laboratories, especially those using sequencing technologies. Sustaining these achievements in the long term and continuing to promote the One Health approach at the laboratory level is fundamental for socioeconomic development, health security, and peace.