Viruscodering

@Gemini 2025-05-25 In Frankrijk is een nieuwe coronavariant vastgesteld, namelijk NB.1.8.1 Het zou om een "subvariant" van de al enkele jaren dominante omicron-variant gaan. Mijn vraag: wat betekent die codering "NB.1.8.1”? Hoe zit dat nummer/coderingssysteem in elkaar en wat was bijvoorbeeld de code van de laatste voorgaande (sub) variant?

In response to your question about the new coronavirus variant NB.1.8.1 detected in France, here's what the codification means and how the numbering system works:

What does the codification "NB.1.8.1" mean?

The code "NB.1.8.1" is part of a hierarchical lineage naming system, primarily the Pango lineage system, used to classify and track SARS-CoV-2 variants and subvariants. These codes indicate their evolutionary relationships.

• NB.1.8.1 is a subvariant of the Omicron variant. More specifically, it is a descendant of the JN.1 variant, which itself is a sublineage of Omicron BA.2.86.

• The numbering system works like a family tree. Each dot separates a new branch or sublineage. So, NB.1.8.1 means it's a sub-branch of NB.1.8, which is a sub-branch of NB.1, and so on. This indicates its position within the complex evolutionary tree of the virus.

According to recent reports (May 2025), NB.1.8.1 is derived from the recombinant variant XDV.1.5.1 and has been designated as a SARS-CoV-2 Variant Under Monitoring (VUM) by the World Health Organization (WHO) due to its increasing global prevalence. It carries several mutations in its spike protein that may increase its transmissibility and potentially reduce neutralization by existing immunity.

How does this numbering/coding system work?

The scientific naming system for SARS-CoV-2 variants, like the Pango lineage system, uses alphanumeric codes to denote lineages and sublineages. This system is crucial for researchers to track genetic changes and evolutionary paths of the virus.

• Pango lineages are assigned to groups of related viruses that share a common ancestor. When a new group of mutations emerges that warrants a new classification, a new lineage is assigned.

• Sublineages are direct descendants of a parent lineage, indicated by additional numbers separated by dots. For example, BA.2.75 is a sublineage of BA.2 (which is an Omicron lineage).

• As the virus evolves and lineages become very long, they are sometimes given shorter alphabetic aliases (e.g., "BA" stands for "B.1.1.529").

The WHO also uses a simplified naming system for "Variants of Interest" (VOI) and "Variants of Concern" (VOC) using letters of the Greek alphabet (e.g., Alpha, Delta, Omicron) to make them easier for the public and media to understand and remember, avoiding the stigmatization associated with geographical names. However, these Greek letter names do not replace the scientific Pango lineage names.

What was the code of the last preceding (sub)variant?

Given that NB.1.8.1 is a descendant of the JN.1 variant, the "last preceding" significant subvariant you might be referring to in its direct lineage, in terms of global prominence and monitoring, would be JN.1.

JN.1 was a rapidly spreading Omicron subvariant that was dominant globally before the emergence of newer descendants like NB.1.8.1. While other subvariants like LP.8.1 and XEC have also been circulating, NB.1.8.1 is specifically noted as a descendant of JN.1.

So, apart from the dots and position of the numbers there doesn't seem to be any system in the codes. Or how can a code jump at once from JN.1 to NB.1.8.1? How can a code jump from nothing to 8 or from JN to NN or other combinated letter combinations like LP or XEC. Do these letters have no meaning at all and are they just made up?

You've hit upon a very insightful point about the apparent "jumps" in the Pango lineage codes! While it might seem chaotic at first glance, there is indeed a system, but it's designed to manage the immense and rapid diversification of the virus.

Here's a breakdown of why the codes appear to jump and what the letters signify:

The Pango Lineage System: A Dynamic Family Tree

The Pango (Phylogenetic Assignment of Named Global Outbreak Lineages) system is designed to track the phylogenetic relationships of SARS-CoV-2. Think of it as a dynamic family tree where new branches (lineages) are named as significant clusters of mutations emerge and spread.

Why Codes Seem to "Jump" (e.g., from JN.1 to NB.1.8.1)

The "jumps" are not random. They represent:

1. New Major Lineages/Aliasing:

   • The Pango system started with A and B lineages. As B.1 diversified extensively, it was given many sub-lineages (B.1.1, B.1.1.7, B.1.1.529, etc.).

   • When a sub-lineage itself becomes very successful and diversifies significantly, it can be aliased (given a new, shorter top-level letter code) to prevent the names from becoming excessively long and unwieldy.

   • Omicron (B.1.1.529) is a prime example. Its sub-lineages like BA.1, BA.2, BA.3, BA.4, BA.5, etc., were created from B.1.1.529. So, "BA" is an alias for B.1.1.529.

   • Similarly, JN.1 is a sublineage of BA.2.86. If JN.1 itself diversifies significantly, its direct descendants might get new aliases.

2. Recombinant Variants: This is a crucial reason for seemingly "new" letter combinations.

   • Sometimes, a single person can be infected with two different SARS-CoV-2 variants simultaneously. When the viruses replicate, they can swap genetic material, creating a recombinant variant.

   • These recombinant variants are given entirely new lineage names, often starting with "X" followed by letters and numbers. For example, XBB is a recombinant of BA.2.10.1 and BA.2.75.

   • The NB.1.8.1 variant, as you noted, is derived from the XDV.1.5.1 recombinant variant. This means it has a distinct genetic makeup that justifies a new top-level lineage designation (NB) rather than simply being a sub-lineage of JN.1, even if JN.1 is its parent in some way. The "NB" here is likely an alias given to a new significant sub-lineage of XDV.1.5.1, or a direct descendant of a lineage that itself spun off from an X variant.

3. Complex Evolutionary Paths:

   • The virus doesn't always evolve in a simple linear fashion. There can be convergent evolution (different lineages developing similar mutations independently) or long branches where a lineage might go undetected for a while and then suddenly emerge with many unique mutations.

   • When a new lineage is identified that doesn't neatly fit under an existing, recent "parent" lineage, it's given a new distinct name.

Do These Letters Have Meaning, or Are They Just Made Up?

The letters are not just made up randomly, but their "meaning" is not always immediately obvious like a phonetic abbreviation.

• Initial Lineages (A, B): These were the very first major lineages identified.

• Aliased Lineages (e.g., BA, BE, BF, BN, CQ, DE, EG, FL, FR, GK, HV, JD, JE, JF, JG, JH, JJ, JK, JL, JM, JN, JP, JQ, JR, JT, JU, JV, JW, JX, JY, KB, KC, KD, KE, KF, KG, KH, KJ, KK, KL, KM, KN, KP, KQ, KR, KS, KT, KU, KV, KW, KX, KY, LA, LB, LC, LD, LE, LF, LG, LH, LJ, LK, LL, LM, LN, LP, LQ, LR, LS, LT, LU, LV, LW, LX, LY, MA, MB, MC, MD, ME, MF, MG, MH, MJ, MK, ML, MM, MN, MO, MP, MQ, MR, MS, MT, MU, MV, MW, MX, MY, NA, NB, NC, ND, NE, NF, NG, NH, NJ, NK, NL, NM, NN, NP, NQ, NR, NS, NT, NU, NV, NW, NX, NY, OA, OB, OC, OD, OE, OF, OG, OH, OJ, OK, OL, OM, ON, OP, OQ, OR, OS, OT, OU, OV, OW, OX, OY, PA, PB, PC, PD, PE, PF, PG, PH, PJ, PK, PL, PM, PN, PP, PQ, PR, PS, PT, PU, PV, PW, PX, PY, QA, QB, QC, QD, QE, QF, QG, QH, QJ, QK, QL, QM, QN, QP, QQ, QR, QS, QT, QU, QV, QW, QX, QY, RA, RB, RC, RD, RE, RF, RG, RH, RJ, RK, RL, RM, RN, RP, RQ, RR, RS, RT, RU, RV, RW, RX, RY, SA, SB, SC, SD, SE, SF, SG, SH, SJ, SK, SL, SM, SN, SP, SQ, SR, SS, ST, SU, SV, SW, SX, SY, TA, TB, TC, TD, TE, TF, TG, TH, TJ, TK, TL, TM, TN, TP, TQ, TR, TS, TT, TU, TV, TW, TX, TY, UA, UB, UC, UD, UE, UF, UG, UH, UJ, UK, UL, UM, UN, UP, UQ, UR, US, UT, UU, UV, UW, UX, UY, VA, VB, VC, VD, VE, VF, VG, VH, VJ, VK, VL, VM, VN, VP, VQ, VR, VS, VT, VU, VV, VW, VX, VY, WA, WB, WC, WD, WE, WF, WG, WH, WJ, WK, WL, WM, WN, WP, WQ, WR, WS, WT, WU, WV, WW, WX, WY, XA, XB, XC, XD, XE, XF, XG, XH, XJ, XK, XL, XM, XN, XP, XQ, XR, XS, XT, XU, XV, XW, XX, XY, YA, YB, YC, YD, YE, YF, YG, YH, YJ, YK, YL, YM, YN, YP, YQ, YR, YS, YT, YU, YV, YW, YX, YY, ZA, ZB, ZC, ZD, ZE, ZF, ZG, ZH, ZJ, ZK, ZL, ZM, ZN, ZP, ZQ, ZR, ZS, ZT, ZU, ZV, ZW, ZX, ZY): These are essentially short-hand aliases for very long lineage names. They are assigned by the Pango team when a particular sub-lineage has become very large and diverse, and continuing to use the full lineage name would make it unwieldy (e.g., B.1.1.529.1.1.5.1.1.1.1.1.1.1). The letters themselves don't typically have a specific mnemonic meaning (like "Omicron Alpha"), but they serve as unique identifiers.

• "X" Designations (e.g., XBB, XEC, XDV): These are specifically reserved for recombinant variants. The "X" clearly signals that the variant is a mosaic of two or more parent lineages. The subsequent letters are assigned to differentiate these recombinant lineages.

In essence, the Pango system prioritizes:

1. Uniqueness: Every assigned lineage name is unique.

2. Hierarchy: The dots indicate descent (e.g., JN.1 is a child of JN).

3. Manageability: Aliases and new top-level names are introduced to keep the system practical as the virus continues to evolve and new significant branches emerge.

So, while "NB" or "LP" might not spell out a specific word, they are part of a systematically assigned code that allows scientists to precisely track the countless branches of the SARS-CoV-2 evolutionary tree.