Interview: LNS Researchers Discuss Coronavirus Sequencing, Omicron Subvariant BA.2

Chronicle.lu recently got the opportunity to speak with two researchers from the National Health Laboratory (Laboratoire national de santé - LNS), Dr Sc Sibel Berger and Dr Daniel Alvarez, about the sequencing of SARS-CoV-2 (the virus that causes COVID-19) in Luxembourg.

Despite the easing of restrictions and the stable situation in hospitals in the Grand Duchy, the number of new COVID-19 cases and incidence rates remain quite high. In their weekly report, Luxembourg's Ministry of Health, the Ministry of Education, Children and Youth, the LNS and the Luxembourg Institute of Science and Technology (LIST) reported a total of 9,550 new cases for the week of 28 March to 3 April 2022; the incidence rate was 1,111.0 per 100,000 unvaccinated people and 1,340.5 per 100,000 fully vaccinated people. On top of this, there is the continued uncertainty linked to the emergence of new Omicron subvariants, such as BA.2.

Chronicle.lu thus reached out to Dr Sc Sibel Berger, Clinical Scientist of the Epidemiology and Microbial Genomics Unit at the LNS department of microbiology, and Dr Daniel Alvarez, Epidemiologist at the LNS department of microbiology, to learn more about new subvariants and the SARS-CoV-2 sequencing process in Luxembourg.

Chronicle.lu: What is the maximum weekly sequencing capacity at LNS?

Dr Sc Sibel Berger: Currently, we can sequence up to 1,330 specimens per week (seven runs of 190 samples with Illumina [innovative sequencing] technology). However, we are working on an additional sequencing technique (Nanopore technology), as well as optimising automation processes, in order to reach the goal sequencing capacity of 2,500 specimens per week. This will result in an improvement not only for SARS-CoV-2 sequencing, but also for other pathogens, like influenza.

Chronicle.lu: How many researchers and technicians are currently involved in the SARS-CoV-2 sequencing process?

Dr Sc Sibel Berger: Six laboratory technicians and five scientists (biologists, bioinformatics, epidemiologists).

Chronicle.lu: Did the researchers and technicians have to undergo special training to accommodate viral RNA sample processing?

Dr Sc Sibel Berger: On the technical side, training for the techniques is required with a high level of expertise to ensure reliable results for RNA samples. Quality work supported by the qualification of the technicians and the implementation of a quality management system. At the level of results analysis, a regular update of the evolution of the circulation of different variants. In addition, [team members] need knowledge in terms of biosafety and risk assessment of the virus and variant tested. In this context, samples must be treated under well-defined and regulated conditions in the laboratory, which must be known by the team.

Chronicle.lu: What is the total cost per sample, from sample collection to sequencing results analysed, and how are these costs shared in terms of the national framework?

Dr Sc Sibel Berger: The total cost per sample has been estimated at €110 with Illumina sequencing technology and is covered by the Ministry of Health. The increase in sequencing capacity has been made possible by European funding (European Centre for Disease Prevention and Control - ECDC).

Chronicle.lu: How many Omicron (BA.1 and BA.2 subtypes) cases have been detected in Luxembourg so far?

Dr Daniel Alvarez: This information is published weekly in the ReViLux report (lns.lu/publications). As of week 11/2022, the LNS has detected 7,450 BA.1 specimens (plus four BA.1.1 specimens, which are a subtype) and 2,696 BA.2 specimens.

Chronicle.lu: Does LNS send samples to other sequencing facilities, for example for low quality samples?

Dr Daniel Alvarez: No, all sequencing is performed at the LNS.