Figure 2.
Sequence alignments highlighting genetic sequence features of the MPXV detected in Kamituga resulting in (A) a single nt mismatch with US CDC recommended generic reverse primer (G2R_G reverse primer) and (B) absence of the US CDC recommended clade I specific forward, reverse, and probe target location (C3L), Democratic Republic of the Congo, 2024
US CDC: United States Centers for Disease Control and Prevention; MPXV: monkeypox virus.
The sequence matching the US CDC primers or probe annealing sites is on the top line, where each nt is highlighted in a different colour. The lines underneath the top line each represent sequences of the MPXV identified in the current study, which are aligned to the sequence on the top line. At each position of a study sequence, identity to the top sequence is represented by a dot. When a difference is a substitution, the nt present in each study sequences is indicated, when a difference is a deletion, this is represented by a dash highlighted in purple.
Visualised by primer-check tool: https://viroscience-emc.shinyapps.io/primer-check/.
