Delta, Omicron Et Al: How The WHO Decides While Declaring New SARS-CoV-2 Lineage As ‘Variant Of Concern’ And ‘Variant Of Interest’

On 26 November, the World Health Organization (WHO) named the new SARS-Cov-2 lineage B.1.1.529 ‘Omicron’ under the Greek letter nomenclature that was adopted by it earlier this year as a uniform system for naming variants of interest and concern. This is the 13th lineage to have got a Greek letter name.

The WHO was panned for skipping the two Greek letters ‘nu’ and ‘xi’ while naming the latest variant which seemed to reinforce the influence China has on the organisation, an accusation that has been levelled repeatedly by the critics against WHO for failing to hold China accountable for its lack of transparency about the virus in the beginning which allowed it to spread all over the world and dilly dallying over investigations to find the true origins of the pandemic specifically whether the virus emerged from the lab, even if unintentionally despite this theory becoming quite plausible in face of mounting evidence.

“Two letters were skipped — Nu and Xi — because Nu is too easily confounded with 'new' and Xi was not used because it is a common surname and WHO best practices for naming new diseases (developed in conjunction with FAO and OIE back in 2015) suggest avoiding 'causing offence' to any cultural, social, national, regional, professional or ethnic groups,” the WHO clarified in a statement.

Nonetheless, the actual surprising element about Omicron was how quickly it got designated as a ’variant of concern’ (VoC). The WHO declared it as a 'variant under monitoring' on 24 November and as a VOC two days later which is unprecedented. Usually, a new lineage which has many concerning mutations is designated as a variant of interest (VOI) but this stage was bypassed in case of Omicron. Within a weak of reporting of its lineage (B.1.1.529) to the Pango network, it was declared a VoC. Pango is a network of researchers and is used for identifying and naming lineages of SARS-CoV-2.

To put this in perspective, Delta was declared as a VOI on 4 April and as a VOC on 11 May in a gap of six weeks.

Of course, none of this should be construed to mean that the WHO has acted in haste. In fact, the evidence on Omicron, with staggering 32 mutations in the spike protein alone, so far suggests that WHO’s stance is warranted and it’s good that public health agencies are being proactive. It’s better to err on the side of caution.

A variant is designated as a VOI if it has genetic changes that can potentially affect changes in transmissibility, disease severity, immune escape, diagnostic or therapeutic escape and can cause significant community transmission in various parts of the world suggesting an emerging risk to global public health.

For a variant to be declared as a VOC, it should demonstrate one of the three factors in addition to the characteristics used in VOI classification. First, if there is an increase in transmissibility or detrimental change in Covid-19 epidemiology. Second, if there is an increase in virulence or change in clinical disease presentation. Third, if there is decrease in effectiveness of public health and social measures or available diagnostics, vaccines and therapeutics.

Prima facie, Omicron qualified to be declared as a VOC on more than one count. While virulence of the variant will be clearly known in a few weeks, WHO probably didn’t want to wait and it had more than enough reason to classify it directly as a VOC, bypassing the VOI designation stage.

As Vinod Scaria, scientist at Delhi-based Institute of Genomics and Integrative Biology, and Bani Jolly, a researcher at the same institute write, “The early evidence for Omicron suggested a detrimental change in COVID-19 epidemiology, along with possible increase in transmissibility and decreased effectiveness of vaccines... There were multiple instances of fully vaccinated cases, including where a booster dose had been received. This suggested that the variant poses a higher risk of reinfection and vaccination breakthrough.”

“Of the 32 mutations identified in the Spike protein, a significant large number were associated with immune escape, cell entry as well as better binding to the human receptor proteins. Early structural analysis was also suggestive of better binding to the host receptors, which provided added confidence in the preliminary assessments. The early reports of a number of Omicron cases from different countries in Europe also suggested that the variant was indeed spreading fast,” they add.

Additionally, the graphs below by Financial Times of cases and hospitalisation in Omicron wave in South Africa’s Gauteng province which houses more than a quarter of that country’s population is telling and it shows that WHO was right in its decision to identify it as something that the world needs to be really concerned about.