Pathogen genomics
Genomic surveillance & variant tracking
Sequenced isolates from sentinel labs, lineage assignment, AMR markers, and outbreak phylogenetics — feeding GISAID and PulseNet.
Sequences (30d)
3,182
Lineages active
48
Variants of concern
2
Sentinel labs
34
Emerging signals
- SARS-CoV-2 KP.3.1.1 — 38% prevalence, risingwarn
- H5N1 dairy spillover — 4 new sequences (clade 2.3.4.4b)warn
- C. auris clade III — 2-hospital cluster, Atlantawarn
- Salmonella Newport — multistate (PulseNet match)info
AMR marker surveillance
- blaKPC carbapenemases · 142 isolates (+18% QoQ)
- mcr-1 colistin resistance · 6 isolates
- vanA enterococci · 88 isolates
- NDM in Klebsiella · 31 isolates
Data sharing
- GISAID submissions: 612 this week
- NCBI SRA: 480 uploads
- PulseNet AMRFinder: nightly
- Pathogen Detection pipeline: green