INTRODUCTION

It's been chaotic to understand the nomenclature of variants of the Novel Corona Virus. There had been recent announcements by WHO regarding the new Nomenclature of the virus. Regular tracking might not have been possible for you to analyse the changes in the naming of the virus. Let's understand why WHO has updated the Nomenclature system and how it is done. Also, what was the need for such a nomenclature when we already had one? Further, we will see how are Viruses named.

Who names Viruses and Diseases?

There are different processes, and purposes, for naming viruses and diseases.

Viruses are named based on their genetic structure to facilitate the development of diagnostic tests, vaccines and medicines. Virologists and the wider scientific community do this work, so viruses are named by the International Committee on Taxonomy of Viruses (ICTV)

Diseases are named to enable discussion on disease prevention, spread, transmissibility, severity and treatment. Human disease preparedness and response is WHO’s role, so diseases are officially named by WHO in the International Classification of Diseases (ICD).

ICTV announced “severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)” as the name of the new virus on 11 February 2020.  This name was chosen because the virus is genetically related to the coronavirus responsible for the SARS outbreak of 2003.  

The official names at present  are: 

  • Disease Coronavirus disease -2019 (COVID-19) Virus 
  • Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Naming  the  SARS-CoV 2 Variants 

Viruses constantly change through mutation, and new variants of a virus are expected to occur. Sometimes new variants emerge and disappear. Other times, new variants persist. Multiple variants of the virus that causes COVID-19 have been documented during this pandemic. So it becomes very important to name them in an organised manner.

Scientists name variants of SARS-CoV-2  on basis of one lineage and two clades.

1).Pango lineage( Phylogenetic Assignment of Named Global Outbreak Lineages)  

2).Nextstrain clade   

3).GISAID clade

Here we will be understanding the Next strain  and Pango lineage (more common to the general public than GISAID)

PANGO LINEAGE 

General naming conventions:

• Pango lineage names comprise an alphabetical prefix and a numerical suffix. The alphabetical prefix contains Latin characters only which are case insensitive.

• The letters I, O and X are not used in the prefix of the names of standard lineages.

• Each dot in the numerical suffix means “descendent of” and is applied when one ancestor can be identified. So lineage B.1.1.7 is the seventh named descendent of lineage B.1.1 and C.1 is the first-named descendent of lineage C.

•The alphabet B.1 denotes that the variant includes an outbreak in Italy in 2020 and is the first descendent of B lineage. 

• The suffix can contain a maximum of 3 hierarchical levels, referred to as the primary, secondary and tertiary suffixes.

(i.e the Pango system can only have 3 dots. You will never find more than 3 dots in Pango nomenclature).

• To avoid four or more suffix levels, a new lineage suffix is introduced, which acts as an alias. For example, C is an alias of B.1.1.1 hence the descendent of B.1.1.1 is called C.1 (rather than B.1.1.1.1). Consequently, the name C, by itself, is never directly applied to a sequence.

•Similarly B.1.351 is the 35th descendent of the virus that caused the Italian Outbreak.

• In some instances, it is not possible to unambiguously identify an ancestral lineage within the Pango nomenclature for a given lineage of interest. This is the case for lineages A and B, because of their position near the root of the phylogeny. For these “special case ancestors”, the alphabetical part alone can be applied directly to sequences. In all other cases, the suffix is mandatory.

NEXT STRAIN CLADE

Nomenclature proposal has the following objectives:

label genetically well-defined clades that have reached significant frequency and geographic spread,

allow for transient clade designations that are elevated to major clades if they persist and rise in frequency,

gracefully handle clade naming in the upcoming years as SARS-CoV-2 becomes a seasonal virus.

Number prefix tells the year of origin of the variant. And the letter tells the clade.

It should be noted, however, that these mutations are only meaningful in that they define the clade; no other functional or epidemiological significance should be attributed to them. 

The first two clades are 19A and 19B. These clades were both prevalent in Asia during the first months of the outbreak. The next clade that was named is 20A corresponding to the clade that dominated a large European outbreak in early 2020.

The clade definitions are coded in as a tabular file that defines a genotypic signature for each clade. We provide a script that generates a table with clade assignments for a set of sequences.

Limitation of Next strain clade comes into play when the variants with genomic sequences altered at positions like 501 come into play. 

GENERAL NAMING FOR SCIENTIFIC COMMUNITY 

A variant like B.1.351  is called 501Y.V2(earlier it was named as N501Y) based on the genomic sequence. This mutation replaces the Asparagine(N) amino acid found at position 501 of spine protein with Tyrosine(Y). The letter V2 denotes the second variant of that particular mutation...This kind of naming is important for scientists to study regular mutations.

CATEGORIZATION OF VARIANTS

WHO has categorized the variants into Variants of Interest and Variants of Concern.

Variants of Concern 

A SARS-CoV-2 variant that meets the definition of a VOI (see below) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance: 

Increase in transmissibility or detrimental change in COVID-19 epidemiology; or 

Increase in virulence or change in clinical disease presentation; or 

Decrease in the effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.  

B.1.1.7, B.1.351, P.1, B.1.617.2 are under VOC.

*Refer to table 2

Variants of Interest 

A SARS-CoV-2 isolate is a Variant of Interest (VOI) if, compared to a reference isolate, its genome has mutations with established or suspected phenotypic implications, and either:  

has been identified to cause community transmission/multiple COVID-19 cases/clusters, or has been detected in multiple countries; OR  

is otherwise assessed to be a VOI by WHO in consultation with the WHO SARS-CoV-2 Virus Evolution Working Group. 

B.1.427, B.1.525, P.2, B.1.526, P.3 etc  are under VOI

*Refer to table 1


RECENT CHANGES BY WHO

Names like B.1.1.7 or 19A etc for different variants in difficult for the general public to remember. Also, these scientific names are important only for the scientific community to analyse the variants in the entire world. So WHO came with some common names to these variants which would be easy for the general public to remember. The names now suggested are alpha, beta, gamma, delta etc


The list is as follows:

Variants of Interest (VOI) (table1)


Variants Of Concern(VOC)(table 2)


Sources-  

  • https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/      
  • https://www.nature.com/articles/d41586-021-01483-0 Pango Lineage Nomenclature: provisional rules for naming recombinant lineages - SARS-CoV-2 coronavirus - Virological 
  • Explained: What is the Delta variant of Covid-19, and why it is a concern? | Explained News, The Indian Express
  • Year-letterGenetic Clade Naming for SARS-CoV-2 on Nextstrain.org
  • https//en.wikipedia.org/wiki/Clade