COVID-19: 2 years into pandemic, original virus nowhere as variants take over

Data from GISAID has revealed the current dominance of the GK clade, to which the Delta variant belongs, in nearly every continent

By Taran Deol
Published: Monday 29 November 2021

It was almost two years ago that a mysterious virus emerged in Wuhan in China’s Hubei province and soon spread worldwide. Now, as the world prepares for another bout with the novel coronavirus disease (COVID-19), the original strain is nowhere to be seen.

According to the nomenclature set by the Global Initiative on Sharing Avian Influenza Data (GISAID) — the world’s largest database of novel coronavirus genome sequences — the S and L clades of the SARS-CoV-2 virus were found at the beginning of the pandemic.

A clade is “a group of organisms that all originate from a common ancestor.” During the early days of the pandemic, while S remained prevalent, L split into G and V, after which G split into several other branches.

Data from GISAID — visualised by the Computational Bioscience Research Center at King Abdullah University of Science and Technology in Saudi Arabia — reveals the current dominance of the GK clade, to which the delta variant belongs, in nearly every continent. 

In Africa, its proportion is 34.41 per cent, in Asia it is 52.04 per cent, in Australia and Oceania it is 51.17 per cent, in Europe it is 51.16 per cent and in North America, it is 53.17 per cent.

South America is the only continent where the lambda variant, a variant of interest (VOI) first found in Peru in December 2020, dominates at 53.91 per cent. Here, the GK clade accounts for 24.99 per cent.

The WHO’s latest weekly epidemiological update on COVID-19 from November 23 also maintains the delta variant continues to dominate across the globe “with the prevalence of other variants continuing to decline.”

The GRY clade’s proportion, to which the UK variant belongs, stands at 27.65 per cent in Europe, followed by 17.08 per cent in Asia, 13.38 per cent in North America and 5.15 per cent in Africa. Its presence in South America and Australia and Oceania is extremely low, at 0.16 per cent and 1.31 per cent respectively.

In Africa, the beta variant — first found in South Africa in December 2020 — belonging to the GH clade is most rampant after the delta variant at 16.2 per cent. Its proportion in other continents is less than 5 per cent, barring North America where its figure stands at 7.23 per cent.

The original strain was in circulation in early 2020 after which the G clade took over, according to GISAID data. The original strain was in high proportions and took longer to phase out in Asia, while the G clade took over rapidly in North America.

The L and S clades were hardly in circulation in South America, Africa and Oceania and were quickly replaced by G clades. In January 2021, the L and S clade’s presence had come down to 1.2 per cent and 2.1 per cent respectively.

New variant 

The WHO has recognised five variants of concern (VOC) and two VOIs in the nearly two years since COVID-19 hit. 

The new ‘omicron’ variant — B.1.1.529 — was first reported to the WHO November 24 from South Africa. The body noted in its statement November 26:

Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa.

It also underlines how a rise in COVID-19 cases in South Africa coincides with the detection of a new variant. Cases have increased by four times in the country in the past two weeks, as they did when the delta variant was detected.

This trend is similar to how the 1918 Spanish Flu became deadlier the second time around. Much like COVID-19, rediscovered lung samples hint the Spanish Flu virus too mutated to infect humans more severely.

Sébastien Calvignac-Spencer, a virologist at Berlin’s Robert Koch Institute accidentally found several lung specimens from 1918 at the Berlin Museum of Medical History of the Charité.

His work is yet to be peer-reviewed. But his study brought the number of complete 1918 flu genomes to just three, adding a 17-year old girl who died in Munich to the list.

The first two were from New York and Alaska. His findings revealed the virus found in the 17 year-old-girl was only half as active as compared to the genome found in Alaska — hinting that the virus adapted to infect humans more severely.

The nucleoprotein from the first wave virus resembled flu viruses infecting birds. Scientists have found that over time, the virus mutated to better adapt to the human body. What the COVID-19 virus is doing is similar and better documented.

The WHO classifies a variant as a VOC when it exhibits one or more of the following changes:

Increase in transmissibility or detrimental change in COVID-19 epidemiology, increase in virulence or change in clinical disease presentation, decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.

There is yet to be any consensus regarding vaccines’ efficacy against the new variant but concerns remain. “They (mutations) have not been observed in this combination before, and the spike protein alone has over 30 mutations. This is important, because the spike protein is what makes up most of the vaccines.”

Also, Omicron’s detection comes at a time when several countries have begun administering booster doses in the backdrop of a waning immunity against COVID-19. While several studies have revealed that antibodies reduce over time — a perfectly normal response — they are not the body’s only means to fight off an infection. The memory B and memory T cells are responsible for generating an immune response when infected.

A vaccine’s role is not to prevent infection at all but to prevent severe disease and death, which the COVID-19 vaccines have shown they can do. However, Gavi the Vaccine Alliance, notes that “booster doses may be beneficial for people who are extremely vulnerable or immunocompromised,” but it remains unclear for how long it remains effective.

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