How NPHIs Can Improve Genomic Surveillance of SARS-CoV-2

On June 30, 2021, IANPHI hosted a webinar to understand how national public health institutes (NPHIs) can further develop genomic sequencing of SARS-CoV-2 as part of their surveillance systems, and how regional and international collaboration can support the development of genomic sequencing. 

Moderated by Dr. Jinal Bhiman from the National Institute for Communicable Diseases of South Africa, the webinar offered case studies presentations from INSP Burkina Faso, Argentina ANLIS, and Denmark SSI on their experience with genomic sequencing and surveillance, their best practices, the gaps they identified and the role of regional and international collaboration in the development of capacities in this field.

A panel discussion followed with experts from Africa CDC, PAHO, CARPHA and NIH Pakistan to exchange ideas about ways international or regional networks and cooperation can participate in reducing regional disparities in the ability to sequence genomes.

NPHI Case Studies

INSP Burkina Faso’s Experience in Genomic Sequencing of SARS-CoV-2 and the Role of Regional and International Cooperation by Prof. Abdoul Salam Ouedraogo, head of Burkina Faso AMR Reference Lab, Institut National de Santé Publique, Burkina Faso (see presentation)

To execute the pandemic response and the proposed testing strategy, the first challenge faced by the Institut National de Santé Publique of Burkina Faso (INSP) was to establish a network of laboratories. Starting with only one laboratory, Burkina Faso has now 15 laboratories able to perform PCR testing. They are also supported by rapid testing, which can identify cases directly at points of care. The current challenge is the surveillance of variants, in which INSP has taken on the role of coordinating the process and of providing technical support. International collaboration has also played an important role in the development of genomic sequencing in Burkina Faso. The project of the African Network for improved Diagnostics, Epidemiology and Management of common Infectious Agents (ANDEMIA) has been of great value. Another important collaboration was developed with the Medical Research Council of Gambia that offered training for laboratory staff in Burkina Faso. The next steps are the continuous improvement of technical capacities and the training of human resources. The collaboration across the international networks is an important factor in these improvements.

Genomic Surveillance of SARS-CoV-2 in Argentina by Dr. Claudia Perandones, director of the Executive Unit for Higher Education and Training, Administración Nacional de Laboratorios e Institutos de Salud, Argentina (see presentation

In Argentina, genomic surveillance has been developed through two main strategies: the Argentine Inter-institutional Project on SARS-CoV-2 Genomics (PAIS) and the Genomics and Bioinformatics Platform of the Administración Nacional de Laboratorios e Institutos de Salud “Dr Carlos G. Malbran” (ANLIS-Malbran). On the one hand, the PAIS consortium is dedicated to the surveillance of the community circulation of the COVID-19 variants across the country. Up to June 30, 2021, the PAIS project has allowed to sequence more than 1,200 samples, to develop 10 research protocols and to involve health professionals as well as public and private institutes. On the other hand, the ANLIS-Malbran Genomics and Bioinformatics Platform is dedicated to the evaluation of the variants entering in the country through the allowed entry ports, the suspected reinfections and the infection of vaccinated patients. Up to June, 2021, the platform has allowed to identify ten variants of SARS-CoV-2 in Argentina. Despite this active genomic surveillance, Argentina is facing different challenges related to the difficulty to unify communication criteria, the issue of geographic representativeness and the lack of harmonization in the techniques used for genomic sequencing. From this perspective, genomic surveillance will be a useful tool to develop both vaccination and therapeutic strategies.

Genomic Surveillance of SARS-CoV-2 in Denmark by Dr. Tyra Grove Krause, executive president ad interim, senior consultant, specialist in Public Health Medicine, Infectious Disease Preparedness, Statens Serum Institute, Denmark

Early 2021 Denmark avoided a third COVID-19 infection wave thanks to the country’s high capacity in both PCR testing and antigenic testing. The test capacities are up to 4 million tests per week and the aim is to sequence all PCR positive samples. Either the samples are sent to the Staten Serum Institute (SSI) to get sequenced, or the sequencing data is shared on a data platform. The strength of the Danish surveillance system is the possibility to link data from different sources, for example the microbiology database, the national patient register or the civil registration system. Thanks to the connection between these databases, the severity, the transmissibility and the immune escape of new variants can be assessed. One of the Danish challenges remains in the collaboration between the different expert groups. SSI is in charge of risk assessment and is strongly connected with the risk management actors. Furthermore, international collaboration is focused on the area of whole genomic sequencing. The wish is to increase global capacity, in order to share the data more timely and to have a better overview of the circulating variants. Finally, whole genomic sequencing data needs to be linked to other clinical and demographic data for better risk assessment of new variants. For post-pandemic time, data from veterinarian and food safety could strengthen the ability to detect and respond to outbreaks.

Panel Discussion

Panel members included Dr. Yenew Kebede Tebeje, head of Division of Laboratory Systems at the Africa Centres for Disease Control and Prevention, Dr. Massab Umair, senior scientific officer at the National Institute of Health in Pakistan, Dr. Lisa Indar, director of Surveillance, Disease Prevention and Control Division, at the Caribbean Public Health Agency, Dr. Juliana Leite, laboratory specialist, Pan American Health Organization.

The first question focused on the gaps and needs in genomic sequencing capacities. Even though laboratory capacities and genomic sequencing have increased, there is still a need in further developing technical expertise to analyze and interpret data as well as financial support.

The second discussion topic examined how international and regional networks could participate in reducing disparities. The importance of not only to create new networks, but also to strengthen those that are already in place, was pointed out. One other important step is to facilitate the exchange between those networks, for example by standardizing methodology and protocols. Another is the training of human resources to increase capacities in each country, which will strengthen the whole network. Within the African Union for example, the network works on different levels to provide support and capacities where it is needed. Additionally, a private-public partnership has proven to be efficient to build laboratory capacities and to reduce costs of genomic sequencing.

Then, it was discussed what a network such as IANPHI could do at regional and international levels to support the networking of NPHIs. The panelists saw potential in providing a platform where experiences, challenges and best practices can be shared, as well as a platform for training, especially in bioinformatics and data interpretation. Moreover, it was pointed out that IANPHI has a leverage position, as it brings NPHIs from all over the world together and can therefore advocate for genomic surveillance as a form of disease control and outbreak response.

Another question was raised concerning the role of the European Center for Disease Prevention and Control (ECDC) in cross-border risk assessment. European NPHIs have ongoing discussion with ECDC and the WHO Regional Office for Europe and it was suggested that they be completed by some quicker solutions that can address the changing situations. A proposal would be to have a platform where information about new variants can be shared in a timely manner. 

Finally, it was once again underlined that the pandemic being a global issue, networking and information sharing are paramount. Information sharing must not only rely on the creation of new platforms but also use and strengthen those that are already in place.

Watch the Full Webinar

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