What is in a name ?

Nada, said the Bard  400 odd years ago and we believed .  We believed that   the pathogen that causes Covid pandemic , would  by any other name  be   dangerous to humanity.  So when the  pandemic took us by surprise and shook us top to toe, we referred  to  the   variants of concern (VOC)  by the country where they  were first detected and identified.  Thus  we  discussed at length about  the UK ,  Indian ,  South African and   Brazilian  variants as   an easier  alternative  to the  string of alphanumerics such  as B.1.1.7 or B.1.167.2 etc.   Because a dot or a number this way or that  and one would have gotten it all wrong. Though the general public was comfortable  to use the simple GI tags,  several country heads rebelled and  protested against this geographical labelling.  For the  first time perhaps being bestowed with a  GI tag was no honour.  To settle matters amicably, the    World Health Organisation  announced its  decision to use Greek alphabets to indicate  the SARS-CoV-2 variants. This decision was not taken in a hurry or in  isolation  but  after much deliberations    with agencies such as  the  Virus Evolution Working Group, the  WHO COVID-19 reference laboratory network, representatives from  the current scientific nomenclature groups and experts and organisations  from several  countries.   As stated by WHO, the idea  was to come up with easy-to-pronounce and non-stigmatising labels for the  variants.  The Greeks have so far not protested against the (mis)use of their alphabets !  

Thus B.1.1.7 which was  popularly known as the UK variant has been renamed as  the Alpha variant, B.1.351, the  South African variant  becomes the  beta  variant,   P.1 the Brazil variant becomes the  Gamma  variant  and B.1.617.2,  the Indian variant becomes  delta variant.    Scientific communities will continue to use the   alphanumeric notations known as the Pango Nomenclature because those are loaded with information.   

To study variants of a given strain, scientists  generally   draw up a family trees that clearly depict the immediate ancestors  and their descendants in other words, the lineage.   These are  called  phylogenetic clusters or clades.  The blue, green and orange  blocks below depict typical family clusters.

A typical phylogenetic tree
Courtesy: wikipedia

SARS-CoV-2 virus has been  unusual in many of its characteristics,  especially  the speed with which it mutates.  A simple family tree as shown above was found grossly  inadequate.   It became  an absolute necessity  that a dynamic  grouping system be in place to accommodate the  rapidly  increasing variants.  A group of scientists in U.K .  developed  the Pangolin or Pango  system  (Phylogenetic Assignment of Named Global Outbreak LINeages) of nomenclature.  

During  the initial days  of the outbreak of the   pandemic in  Wuhan  two types of  dominant  variants   were identified:  A and B. (Scientists till now haven't been able to zero in on their common ancestor.  That is another story, let us not go there now).    Several  direct  lineages of  B have so far been identified, of which   B.1 is the most predominant line.  It has   1000+ sub-lineages  and sub.sub-lineages.  In the Pango system, the  alphabetic prefix denotes clear ancestry,  each dot means next generation and the number denotes the order in which it was identified.   Thus B.1, is the first identified  of the 4009  direct descendants  of B  and B.1.617 is the 617th identified descendant of B.1.   In order to avoid unwieldy  long numbering, each cluster has just three levels, primary, secondary  and tertiary. Example  B1, B.1.1. and B.1.1.1  form  one cluster.     B.1.1.1. takes  on n alias   C and   its first identified descendant is  designated as C.1  and not   B.1.1.1.1 .     

The Pango is dynamic and flexible enough to accommodate all variants identified so far and yet to be . Though a bit labyrinthine at first glance it is simple and easy to navigate.   

Tree diagram of lineages of SARS-CoV-2
according to the Pango nomenclature system.
Courtesy: MinMaj7th, wikipedia

There are other classification systems too such as the GISAIDS and Nextstrain.  All these provide    specific and detailed  informations on genetic and epidemiological features and  spread of a pathogen. 

Tailpiece

The James Webb Space Telescope (JWST), will soon be renamed.  Several allegations have surfaced  that   James Webb,  head  of NASA during   1961-68,   didn't  treat  gay and lesbian people  properly.   The JWST, set to peep into the unchartered regions of the cosmos  is  NASA’s upcoming prestigious  astronomical project. 

REFERENCES:

1. Tracking SARS-CoV-2 variants

2.A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

3. Pango Lineage Nomenclature: provisional rules for naming recombinant lineages

4 .GISAID Mission

5. Nextstrain: real-time tracking of pathogen evolution