With input from Dr Monica Vasudev

1325: Scientists from Britain have found emerging evidence that the new, more transmissible mutant coronavirus strain spreading across the country might be 30% more fatal.

Chief medical officer Chris Whitty and chief scientific advisor Sir Patrick Vallance expressed concern that the existing vaccines might not work against other variants that have been detected in South Africa and Brazil.

The British strain, named B.1.1.7, is nearly 70% more transmissible compared to the original virus and is accountable, in part, for a rise in cases. Scientists suggest that the new strain might also heighten the death rate by around 30%.

Considering a man in his 60s, for every 1000 people getting infected, around 10 would probably die with the virus. However, with the new variant, for 1000 people infected with the virus, around 13 or 14 people would be expected to succumb.

Experts were asked by the government’s New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) to evaluate data about the new variant and if it was causing more deaths. The London School of Hygiene and Tropical Medicine revealed that the strain could be 1.35-fold more fatal. Scientists from Imperial College London provided a figure of 1.29 to 1.36. The University of Exeter reported that the risk of death could 1.91-fold higher.

Prime Minister Boris Johnson signalled added border controls owing to concerns over variants first detected in South Africa and Brazil. According to scientists, those two strains are not more transmissible than the UK strain; however, there are increasing concerns that they may not respond to the newly-approved vaccines. The variants have some features which could mean that they might be less susceptible to the vaccines.

Forty four to 71 cases of the South African variant have already been detected in the UK. Pfizer and AstraZeneca have stated that the current products can be adjusted to respond to new variants; however, there could be issues due to more resistant strains for the millions who have already received the shot.

In a leaked video, Health Secretary Matt Hancock was seen telling travel agents that the South African variant might diminish the vaccine efficacy by about 50%.

Both the South African and Brazil variants have more differences in shape. This could mean that the antibodies might recognize them differently. Hence, laboratory studies are pointing to decreased binding.

Brazil Strain

Just like the strains of novel coronavirus that were first identified in the U.K. and South Africa in late 2020, the variant that originated in Amazonas, termed P.1, has an array of mutations, including on the spike protein. Another Brazilian variant, termed P.2, which has been detected in Rio de Janeiro state, is not yet of particular concern to scientists.)

aa:orf1ab:S1188Laa:orf1ab:K1795Qdel:11288:9aa:S:L18Faa:S:T20Naa:S:P26Saa:S:D138Yaa:S:R190Saa:S:K417Taa:S:E484Kaa:S:N501Yaa:S:H655Yaa:S:T1027Iaa:orf3a:G174Caa:orf8:E92Kaa:N:P80R

Brazilian lineage with variants of biological significance E484K, N501Y and K417T: P.1 lineage is a pseudonym of lineage B.1.1.28.1. When the lineage hierarchy attains a certain depth (length of 5) an alias is given to lineage names in order to prevent them from becoming too long.

A new variant was identified in December in Manaus, Amazonas state, north Brazil, where there were previous estimates of high attack rates. The new lineage, termed P.1, has unique lineage defining mutations, which include mutations of biological significance like E484K, K417T, and N501Y. This lineage was detected in 42% of RT-PCR positive samples obtained from 15 to 23 December. However, it was not detected in 26 publicly available genome surveillance samples that were obtained in Manaus from March through November 2020. These point to local transmission and a recent rise in the frequency of a new lineage from the Amazon region. The higher diversity and the earlier sampling dates of P.1 in Manaus validate the travel information of recently detected cases in Japan, and indicate that the direction of travel was Manaus to Japan. The emergence of variants with several shared mutations in spike is concerning as it indicates convergent evolution to a new phenotype, which could have increased transmissibility or propensity for re-infection of individuals.

Convergent mutations that are shared between P1, B.1.1.7 and B.1.351 lineagesThe P.1. lineage from Manaus and the B.1.1.7 first detected in the UK share the spike N501Y mutation and deletion in ORF1b (del11288-11296 (3675-3677 SGF).

The P.1. lineage and the B.1.351 (also known as 501Y.V2) lineage described in South Africa share three mutation positions in common in the spike protein (K417N/T, E484K, N501Y). The P.1 and the B.1.351 lineage also carry the orf1b deletion del11288-11296 (3675-3677 SGF).

The mutations/deletions that P.1, B.1.1.7, and the B.1.351 lineages share seem to have appeared independently. Both mutations shared between P1 and B.1.351 seem to be tied to a rapid rise in cases in locations where previous attack rates are thought to be very high. It thus becomes important to investigate if there is an increased rate of re-infection in previously exposed individuals.

S Africa: 501.V2: Main Substitution:  N 501Y, Other substitutions: K417N Lysine with Asparagine, E484K: Glutamic acid with Lysine

Sources: The Sydney Morning Herald; Time; https://cov-lineages.org/global_report_P.1.html; https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586]

Dr KK Aggarwal

President CMAAO, HCFI and Past National President IMA