Variant Naming: WHO Greek, Pango, and Nextstrain Compared

When you read that "JN.1 is a descendant of BA.2.86 within clade 23I (Omicron)," three different naming systems are running in parallel. The same SARS-CoV-2 variant has a Pango lineage, a Nextstrain clade, and might have a WHO Greek letter if it earned one. Each system answers a different question, which is why all three persist instead of consolidating.

Reading variant news without understanding the naming systems is like reading airline schedules without knowing the airport codes. This post fits with the genomic surveillance overview and antigenic drift vs shift, inside the broader disease severity framework.

Key Takeaways

• WHO Greek letters (Alpha, Beta, etc.) are public-communication labels for variants of concern.
• Pango lineages (B.1.1.529, JN.1) are scientifically precise descent names assigned to each evolutionary branch.
• Nextstrain clades (23I, 24A) are timestamped major branches optimized for tree visualization.
• WHO retired active Greek lettering for SARS-CoV-2 in March 2023 as monitoring shifted to Pango lineages.
• Influenza uses an entirely separate system based on antigenic typing and HA/NA subtypes.
• Different systems serve different audiences: clinicians, virologists, and the public each need different precision.

What is the Pango system?

Pango (Phylogenetic Assignment of Named Global Outbreak Lineages) is the descent-based naming system for SARS-CoV-2 introduced by Rambaut and colleagues in 2020. Lineage names follow a tree structure: B.1 begat B.1.1, which begat B.1.1.7 (Alpha), which begat B.1.1.7.1, and so on. Aliases (XBB, JN, KP) compress long names once they pass three sublevels.

The Pango committee assigns new lineages based on phylogenetic distinctness and circulation pattern. As of mid-2026, over 9,000 SARS-CoV-2 lineages have been named. The full lineage tree is available at cov-lineages.org.

Pango is the standard for scientific literature, public health surveillance, and PCR variant reporting. It is precise but unwieldy for headlines. "KP.3.1.1" tells a virologist exactly where on the tree the variant sits but means little to a general audience.

What is the Nextstrain clade system?

Nextstrain clades group Pango lineages into broader, time-stamped categories named YearNumberLetter format. For example, clade 23I covers BA.2.86 and its descendants including JN.1. Clade 24A covers KP.2 and its descendants. A new clade is named when a lineage reaches at least 5 percent global prevalence or shows enough divergence to warrant its own visualization branch.

The Nextstrain approach optimizes for tree visualization at nextstrain.org. Each clade is a meaningful branch on the global phylogenetic tree. The system is coarser than Pango by design.

Clades are useful for situational awareness ("what is circulating now?") more than precise tracking. Clinicians and the public often see clade-level reporting in WHO weekly updates and journal review articles.

What were the WHO Greek letter labels?

WHO introduced Greek letter labels for SARS-CoV-2 in May 2021 to address two problems: stigma from geographic names (the "UK variant", the "South African variant") and complexity of Pango names for public messaging. Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) were the consequential variants of concern.

WHO designated 5 Variants of Concern, several Variants of Interest, and Variants Being Monitored. As Omicron's descendants proliferated and no clearly distinct successor emerged, WHO retired active Greek lettering for new SARS-CoV-2 variants in March 2023. Subsequent variants are tracked by Pango lineage and Nextstrain clade only.

The retirement does not erase existing labels. Omicron is still Omicron. But there will likely not be a Pi or Rho unless an entirely novel variant emerges.

How does influenza naming differ?

Influenza uses an entirely different nomenclature based on antigenic subtypes plus geographic and temporal markers. The format is: Type/Host/Geographic Origin/Strain Number/Year (HA Subtype, NA Subtype). For example, A/California/07/2009 (H1N1) is the strain that caused the 2009 pandemic.

Flu types A, B, C, and D are based on nucleoprotein. Subtypes are defined by HA (hemagglutinin, 18 subtypes) and NA (neuraminidase, 11 subtypes). H5N1, H7N9, H3N2, and H1N1 are subtypes. Specific strains within a subtype have the full geographic-temporal format.

For pandemic readiness, WHO and CDC track avian H5N1 and H7N9 most closely. The current H5N1 panzootic involves clade 2.3.4.4b, named within the avian H5 nomenclature, which is separate again from human influenza naming. The H5N1 pandemic risk post covers the threat assessment.

Why do three systems exist?

Each system optimizes a different goal. Pango optimizes for tracking every meaningful descent. Nextstrain optimizes for visualization at the right level of zoom. WHO Greek letters optimize for public communication during emergencies. Forcing all three into one would lose either precision, readability, or accessibility.

Compare it to map projections. Mercator preserves angles for navigation. Equal-area projections preserve land mass for comparison. Globes preserve everything but are impractical. Each exists because each does its job better than the others would in that role.

The systems also evolved on different timelines. Pango was designed during the early pandemic. Nextstrain's clade system existed for influenza before SARS-CoV-2. WHO Greek letters came later as a communication layer over the existing scientific systems.

Which system should you use?

Use whichever system fits your audience. In a paper, use Pango with parenthetical clade and Greek if applicable: "JN.1 (clade 23I, descendant of B.1.1.529 / Omicron)." In a news article, lead with the Greek or familiar lineage shorthand: "JN.1, an Omicron descendant." In casual conversation, just say "the current variant" and explain why if context demands.

For PandemicAlarm event tracking, we use Pango plus Nextstrain clade for technical accuracy, and reference the most recent WHO Greek letter when the variant has one. This keeps the underlying science traceable while remaining readable.

The systems will keep diverging as new viruses get named with different conventions. Mpox uses Clade I, Clade II with subclades Ia, Ib, IIa, IIb. The Mpox clade Ib news post covers the current Mpox situation. Each pathogen ends up with its own taxonomy reflecting its evolutionary structure.

FAQ

Why did WHO stop assigning Greek letters?

The Greek system was designed for a small number of clearly distinct variants. Once SARS-CoV-2 evolved into a continuous swarm of Omicron descendants without a clean successor variant, Greek letters lost their utility. WHO formalized the pause in March 2023 and shifted communication to Pango and Nextstrain naming.

Will the alphabet run out?

The Greek alphabet has 24 letters and WHO used 13 (Alpha through Omicron, skipping Nu and Xi for sensitivity reasons). If WHO resumes lettering for a future pandemic, they would likely start a new alphabet rather than continue past Omicron. The whole question is academic until a clearly distinct new variant emerges.

Why are Nu and Xi skipped?

Nu was skipped because it sounds like "new" and would cause confusion. Xi was skipped because it is a common surname including that of the Chinese president, and WHO policy avoids stigmatizing names. Both decisions came from the May 2021 naming policy.

How are flu variant labels different from COVID?

Influenza nomenclature predates the SARS-CoV-2 systems by decades. Flu is named by type, host, location, strain, year, and HA/NA subtype. It is more detailed at the strain level but groups variants less aggressively. There are no Greek letters for flu.

Where can you check a variant's lineage?

cov-lineages.org for SARS-CoV-2 Pango lookups, nextstrain.org for live phylogenetic trees, and the WHO Tracking SARS-CoV-2 variants page for the official designations. GISAID provides the raw sequence data underlying all three systems.