SARS-CoV-2 sequencing in Denmark with Mads Albertsen
Mads Albertsen joins the hosts to explain how his research group became part of Denmark’s national SARS-CoV-2 sequencing effort. Recorded on 9 March 2021, the discussion covers sample logistics, changes to the ARTIC protocol, sequencing capacity and the legal barriers to using linked health data. It shows why successful surveillance depends on much more than access to sequencing instruments.
Listen to Episode 52: SARS-CoV-2 sequencing in Denmark with Mads Albertsen on SoundCloud
In this episode
From university closure to national surveillance
When Denmark closed university laboratories in March 2020, Albertsen asked a funding body whether he could redirect an existing grant and staff towards SARS-CoV-2. He contacted hospitals and the national laboratory, offering to sequence whatever samples they sent. His university reopened the laboratory for COVID work, and the group generated its first genomes within days using the ARTIC protocol and Nanopore sequencing.
Legal arrangements took longer than laboratory setup. Anonymised test samples could be sequenced within a week, but another two weeks were needed before the group could provide data linked to patient information. The shift also paused a project intended to sequence 10,000 samples across Denmark to investigate microbial diversity.
Why sample logistics determine turnaround
The group receives plates of extracted RNA rather than handling the original diagnostic samples. Albertsen describes plates containing 88 samples, four negative controls, one positive control and two blank positions for concentration measurements. Standardised plates can pass through the workflow without rearrangement.
Denmark’s community testing track uses large automated laboratories near the national laboratory. Positive samples are re-extracted and prepared for sequencing. Hospital samples require more manual handling and transport; collecting the original samples and re-extracting them proved easier than retrieving diagnostic RNA. Reported turnaround from sampling to sequence was about five days for community testing and ten days for hospital samples in national surveillance. Local hospital sequencing could support same-day turnaround for outbreaks.
Running Nanopore at surveillance scale
Two plates are pooled and divided across two or three MinIONs, reducing the risk that one poor flow cell prevents sufficient data generation. Sequencing starts in the afternoon and stops after 10 gigabases per flow cell or at 6 am the next morning. Predictable delivery matters more than exhausting each flow cell’s capacity. Washed flow cells are retained for development work and emergency use.
At the time of recording, the group was processing roughly 1,000 samples a day, with a potential capacity of 2,500. Each batch takes two laboratory days: cDNA and PCR work first, then pooling, normalisation and Nanopore preparation. During January’s urgent response, the team reached 10,000 samples a week.
Changing ARTIC barcoding and amplicon length
The original workflow’s 24 available barcodes would have required too much laboratory labour at the intended scale. The group instead introduced barcodes during PCR, making around 500 barcodes from ten random nucleotides. It also increased amplicon length to approximately 1,200 bases, using roughly one-third of the ARTIC primers to make better use of Nanopore capacity.
A comparison of around 100 samples gave similar results to the original ARTIC protocol, and missing high-Ct samples did not turn out to be a big problem. Longer amplicons mean a dropout removes more of the genome, but fewer primer sites are exposed to mutations. The group rebalanced poorly performing primers. Albertsen says the method was shared on protocols.io, while fuller write-ups remained unfinished.
Turning sequences into public-health decisions
National surveillance was particularly focused on B.1.1.7 and other variants of concern. Earlier mink-associated variants had prompted increased sequencing in November. Data generated around Christmas and New Year subsequently contributed to decisions to impose stricter lockdowns in Denmark.
One of the hosts explains how hospital outbreak analysis needs more than a lineage label: specialists must interpret clusters, distinguish separate outbreaks and work with healthcare staff. Albertsen identifies a shortage of people able to connect genomic analysis with clinical practice. Looking beyond COVID-19, the conversation considers sequencing for flu and bacterial outbreaks, including metagenomics. He sees sequencing cost as less of an obstacle than developing robust procedures that hospitals can integrate into routine work.
Sharing data and handing over the programme
Denmark’s national laboratory links samples to individuals and health records, while Albertsen’s group connects genome data with healthcare data on its servers. The discussion covers uploads to GISAID and ENA. Around 50,000 sequences had been uploaded after approximately 100,000 samples were sequenced; repeat samples and records that could not be properly linked were among the exclusions.
Legal restrictions remained unresolved, including access to community-testing data for hospital investigations. Analyses could require collaboration with the national laboratory, creating a staffing bottleneck. Albertsen hoped to hand sequencing over to hospitals and the national laboratory by summer. His advice is to acknowledge everyone along the sample-to-action chain and build a team prepared to solve practical problems continually.
Highlights
- 00:01:35 — Redirecting research funding and reopening the laboratory for SARS-CoV-2 sequencing.
- 00:02:38 — Legal agreements needed to connect sequencing with patient information.
- 00:05:35 — Pooling plates across MinIONs and setting overnight sequencing limits.
- 00:07:46 — Automated community testing and the national laboratory’s sample-handling role.
- 00:09:43 — Reported turnaround times for community and hospital surveillance samples.
- 00:14:08 — Moving barcoding into PCR and increasing amplicon length.
- 00:15:27 — The trade-off between fewer primer sites and larger amplicon dropouts.
- 00:18:37 — Daily sequencing capacity and the two-day laboratory workflow.
- 00:23:02 — Filtering uploaded sequences and negotiating limits on metadata sharing.
- 00:25:05 — Plans to transfer sequencing to hospitals and the national laboratory.
- 00:26:54 — Advice on collaboration, acknowledging contributors and solving operational problems.
In their own words
It’s been fun to help out, but of course it’s been a big hit to our normal research.
— Mads Albertsen, 00:04:49
Who is talking
- Mads Albertsen (guest, Center of Microbial Communities, Aalborg University)
- Lee Katz (host)
- Andrew Page (host)
- Nabil-Fareed Alikhan (host)
Tools and resources mentioned
ARTIC protocol, Nanopore MinION, protocols.io, GISAID, ENA.
Questions this episode answers
How did the Danish group modify the ARTIC protocol?
It moved barcoding into PCR and increased amplicon length to approximately 1,200 bases, using roughly one-third of the ARTIC primers. The changes addressed laboratory workload and Nanopore sequencing capacity.
How many SARS-CoV-2 samples could the group sequence?
At the March 2021 recording, Albertsen reported about 1,000 samples a day, with capacity to reach approximately 2,500 if necessary. During an urgent period in January, the team processed 10,000 samples a week.
Why did hospital samples take longer than community samples?
Hospital samples needed more manual retrieval and transport. The community-testing laboratories were highly automated and located next to the national laboratory, supporting a shorter route into sequencing.
What limited the use of sequencing data in hospitals?
The discussion identifies shortages of genomic epidemiology expertise and legal restrictions on sharing linked data. Hospitals could need the national laboratory’s involvement to analyse community and hospital cases together.
This page was written from a machine transcript of the episode and checked against it. Listen to the episode for the whole conversation.
Show notes
Denmark is one of the leading countries in the world forSARS-CoV-2 genomic surveillance. Prof Mads Albertsen chats to us about SARS- CoV-2 sequencing in Denmark, how it got started, logistics, tweaked protocols and things hes learnt along the way. Edited by Niamh Page