diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config
index d889460..6321e8f 100644
--- a/conf/pipeline/viralrecon/genomes.config
+++ b/conf/pipeline/viralrecon/genomes.config
@@ -4,17 +4,41 @@
  * -------------------------------------------------
  * Defines viral reference genomes for all environments.
  */
- 
+
 params {
   // Genome reference file paths
   genomes {
     'NC_045512.2' {
-      fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz"
-      gff   = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz"
+      // This version of the reference has been kept here for backwards compatibility.
+      // Please use 'MN908947.3' if possible because all primer sets are available / have been pre-prepared relative to that assembly
+      fasta            = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
+      gff              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz'
     }
     'MN908947.3' {
-      fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz"
-      gff   = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz"
+      fasta            = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz'
+      gff              = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+      primer_sets {
+        artic {
+          '1' {
+            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.reference.fasta'
+            gff        = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V1/nCoV-2019.primer.bed'
+            scheme     = 'nCoV-2019'
+          }
+          '2' {
+            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.reference.fasta'
+            gff        = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V2/nCoV-2019.primer.bed'
+            scheme     = 'nCoV-2019'
+          }
+          '3' {
+            fasta      = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta'
+            gff        = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed'
+            scheme     = 'nCoV-2019'
+          }
+        }
+      }
     }
   }
 }