With the imminent roll-out of vaccines for protection against the novel coronavirus SARS-CoV-2 in large parts of the world, and a couple of them already deployed in a few countries for emergency use among select cohort groups, it seemed that the world would soon be on top of the COVID-19 pandemic. As in the separate article Professor Gagandeep Kang has described , scientists and industry have worked together to use advanced science and technology to achieve what would have seemed impossible only a few years ago of delivering efficacious vaccines in less than a year’s time, a process known to take a decade or more.
Because of the raging pandemic, the normal time frame for vaccine development was greatly squeezed. There has been a total paradigm shift from the traditional approach in clinical trials, approvals for public deployment and subsequent production. Investments towards R&D have poured in from multiple quarters, trial protocols have been shortened, approvals hastened and the industry too has taken a huge step of investing large sums to set up production infrastructure even before the trials were completed and regulatory approvals obtained. There was belief in the science behind these novel vaccines in the academia, the governments and the industry, and that hope had become a reality just a few weeks ago with the launch of a few vaccines.
But the light at the end of the tunnel which was bright until less than a month ago has dimmed slightly with the emergence of two new variants of the virus, in the United Kingdom and South Africa respectively, which have been found to be more highly transmissible than the original version from Wuhan (and other biologically and epidemiologically inconsequential genetic variants thereof) that the world has braved since December 2019.
Spike in cases in U.K.
In the past couple of months, Britain had seen a rapid increase in COVID-19 cases (Fig. 1), particularly in South East England, with Kent being the most affected. Between the 41st week and 50th week, it increased from 100 cases per 100,000 population to 400 per 100,000 population, the reason for which was immediately unclear. Enhanced epidemiological investigations and genomic analysis were launched to find the basis for this unexplained sudden local spike in the number of cases.
Genome sequencing of virus isolates from these new cases found that over 50 per cent of the isolates had genomes belonging to a new single evolutionary grouping, technically called a phylogenetic cluster. This distinct variant has been named SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, variant 01) and is also sometimes referred to as ‘lineage B.1.1.7’. In its COVID-19 monitoring and surveillance programme, the U.K. has put in place what is called “genomic epidemiology” in which epidemiological data is linked with sequencing data of isolates from a significant percentage of COVID-19 cases. Overall, the rate at which the U.K. has been analysing genomes of COVID-19 cases is around 5-10 per cent, which is quite high compared with most other countries. When the variant was detected, the rate in the region around Kent was about 4 per cent.
To date, for a total of over two million cases, the U.K. has analysed 126,219 genomes (6.3 per cent). This is over 45 per cent of the total of about 275,000 genome sequences submitted to the global genome database called GISAID (Global Initiative on Sharing All Influenza Data). The fraction of the new VUI isolates in the weekly number analysed by the body called COVID-19 Genomics UK Consortium (COG-UK) steeply increased from the 40th week, and is currently over 12 per cent (Fig. 3).
The United States, on the other hand, has a total caseload of over 17 million and has analysed only 51,000 genomes (0.3 per cent). South Africa, which has also detected a new more infectious variant and has 912,500 total COVID-19 cases, has released 2,730 genome sequences (0.3 per cent). India has an abysmally low rate of genomic sequencing of virus isolates from patients. With a total number of cases at over 10.1 million, India has released sequences of only 6,370 genomes (0.06 per cent) so far.
The U.K. perhaps was able to pick up this variant given its very high rate of genome sequencing, which is linked to the epidemiological surveillance system in place. It is quite possible that significant variants (perhaps including this) have been circulating in other populations around the world but missed detection because the genome sequencing rate has not only been low in most countries but also not dovetailed to their COVID-19 epidemiological data gathering, especially when there are sudden local spikes in the number of cases, which have occurred in India, for example.
While surveillance and genomic analyses of the new cohort of recently infected patients in the U.K. (predominantly from South East England) have certainly demonstrated that this new variant is more transmissible, and hence more infectious, answers to other questions about the variant’s biology, such as whether it causes more (or less) severe disease and whether it can evade human natural and/or vaccine-induced immune response, are uncertain. Extensive laboratory and clinical studies are required to unequivocally answer those questions, which undoubtedly will take time.
According to the COG-UK, which carried out the genomic analysis on the new cases of infection, this particular variant is growing in the U.K. about 70 per cent faster than the strain(s) that we have lived with until now. On the basis of this data, the New and Emerging Respiratory Virus Threats Advisory Group (Nervtag) of the U.K. has reportedly said that it is “moderately confident” that this new variant is substantially more transmissible. The fact that the variant was growing exponentially even during the lockdown period gave the Group that moderate confidence to declare that it demonstrated a substantial increase in its transmissibility compared with other variants (carrying mostly harmless genetic changes or mutations) that have appeared during the pandemic. In addition, it also said that the variant had the potential to increase the parameter R-nought (R0), which is a measure of the number of persons that each infected case passes on to, by 0.4 or more than the values observed before this new variant came to light. The higher (than 1) the R0 is, the more widely the virus spreads. As of December 15, over 1,600 individuals had been infected with this variant in the U.K., the earliest case being traced to September 20.
Until now there is no evidence of increased severity of the disease among those infected with this new U.K.-variant. According to a report of the European Centre for Disease Prevention and Control (ECDC), investigations into the properties of this new variant are ongoing and the U.K. has not so far reported adverse clinical observations, such as higher mortality or particularly affected groups. Cases with this variant were, however, seen predominantly in people younger than 60 years (Fig. 2), and it is these cases that are chiefly driving the increase of overall COVID-19 cases in the U.K. as well (Fig. 2). Modelling studies too have shown a strong correlation between the cases with the new variant and the overall increase in the caseload. In Wales, which too has seen a similar spike due to the new variant, the median age of the cases is 41 (range 11-71 years). But as the ECDC report points out, the current assessment that it does not seem to cause severe disease is also questionable because the affected age group is known to be less likely to develop severe disease. So, more clinical studies are necessary to firmly establish this.
While these above cases were concentrated in Kent and in the wider South East England, including regions of London and East England, there are indications of a wider spread across the U.K. and also reports of a few cases in other countries. In Wales, as of December 14, 2020, 20 individuals had been identified with this virus variant. Denmark apparently has identified nine cases, the Netherlands one, and Australia one. There are also media reports of four cases in Belgium.
According to the ECDC report, three sequences from Denmark and one from Australia, from samples collected in November 2020, cluster with the U.K.-variant in the phylogenetic tree. This indicates that international spread has most likely occurred already, although the extent remains unknown, the report says. Besides, of course, there are cases arising from the South African variant. This variant has recently also been seen in a few cases in the U.K. But detailed information about whether its lineage is the same as the UK-variant (lineage 188.8.131.52) and the number of people infected with the SA-variant within South Africa and globally is, however, not immediately available. We will return to the SA-variant later.
Pertinently, as the ECDC report notes, “the [U.K.] variant has emerged at a time of the year when there has traditionally been increased family and social mixing”. So, what seems imminent, given the continuing rapid increase of these variants among the newly infected in the U.K. and South Africa, is that the pandemic is unlikely to die away anytime soon. If it spreads 70 per cent faster than the current variant, it will, in all likelihood, become the dominant form of infection and disease. Even a global second wave of infection spread with this new variant is possible, unless the usual precautions are strictly adhered to and other restrictions on movement are strictly enforced, particularly on international travel between the affected countries and others. This is already happening with the announcement of travel bans between some European countries and the U.K.
Viruses frequently undergo mutations, which occur due to random errors in copying the viral DNA or RNA as they multiply in the host, and these errors accumulate over time. The SARS-CoV-2 undergoes about two mutations (which are generally of the single nucleotide substitution type in the genes coding for amino acids, which are the building blocks of proteins in any organism). But this cluster differs by 29 nucleotides from the original Wuhan strain, according to its preliminary genetic characterisation. This means that the accumulation rate of mutations in this variant has been higher than two substitutions per genome per month.
As mentioned earlier, most nucleotide substitutions are harmless and, therefore, not of concern as they do not change the amino acid that the gene codes for. But when a substitution results in the change of the coded amino acid, the functionality of the corresponding protein may change, and if that is a critical antigenic region of the viral genome, it is concerning. For instance, the flu virus accumulates mutations at such a rate that a new vaccine is required every year. The amino acid substitutions that have no effect on the protein functionality are called “synonymous” mutations and those that do alter the protein function are called “non-synonymous” mutations.
Genetic analysis of the new variant from the U.K. has revealed an unusually large number of mutations in its genome, which include changes that could potentially impact patients’ response to pharmaceutical interventions to the disease. There are in all 23 mutations in this UK-variant, 17 of which are non-synonymous. Over half of these (nine) have been found to be across the Spike protein. S-protein is the stud-like protrusion in the outer envelope of the virus which the virus uses to gain entry into the host’s cells and use the host biochemical machinery to replicate and infect the host. This fraction (9/17) is much higher than what is expected from random mutations, according to the ECDC report. These nine mutations are, in fact, thought to define the variant because, while many of these mutations individually have been observed in other variants as well and have been found to change the functional behaviour of the virus, but not in this combination. So this rare combined effect of these mutations on the S-protein could have a significant health impact.
It would be recalled (“ How a Virus Evolved in a Pandemic ”, Frontline , May 22, 2020) that, during March-April 2020, we had already witnessed the emergence (from Europe) of a new lineage called A2a, with a dominant and defining ‘non-synonymous’ mutation called D614G (where the amino acid Aspartic acid (D) at site 614 in the Receptor Binding Domain (RBD) region of the S-protein was substituted by the amino acid Glycine (G)). The variant having Glycine (G614) was found to be more infectious than the original with Aspartic acid. However, it was also found that the body’s innate immune system was able to produce antibodies against this variant as well. That is, the variant did not evolve to evade the immune system. In fact, the 614G variant was found to be more vulnerable to the neutralising antibodies. In the current new variant, however, studies with other viruses suggest that some of them could be what are called “escape mutations”—those which evade the immune system—and hence the concern for the new variant’s possible significant impact on the pharmaceutical interventions to the disease and thus on the pandemic. The defining nine mutations of the UK-variant which are on the S-protein are: deletion (of gene) at position 69-70, deletion at position 144, N501Y, A570D, D614G, P681H, T7161, S982A and D1118H.
Potential biological effects
Based on previous studies on other SARS-CoV-2 variants, three of these mutations are known to have potential biological effects, according to the preliminary genomic characterisation of the UK-variant by the COG-UK consortium:
1. Mutation N501Y, in which the amino acid asparagine (N) has been replaced by the amino acid tyrosine (Y). Like the mutation D614G, it is also located within the receptor-binding domain (RBD) of the S-protein and has been previously identified as increasing affinity to the ACE2 receptor on the host cells to which the virus binds and enters the cell. That is, this mutation could enable the virus to bind more tightly to the human cells. It is unknown whether tighter binding translates into any significant clinical or epidemiological differences. According to the U.S. Centres for Disease Control (CDC), this mutation has been associated with increased infectivity and virulence in a mouse model.
2. The double gene deletion at position 69-70 of the S-protein has been seen many times before and is likely to lead to conformational (or shape) change in the spike protein, according to the CDC. Perhaps due to this shape change, it has also been described earlier to aid evasion of human immune response in terms of antibodies in some immunocompromised patients.
3. Mutation P681H is immediately adjacent to the site of cleavage of the S-protein into its S1 and S2 sub-regions (a feature absent in other coronaviruses) by the human enzyme furin, which facilitates fusion of the virus with the human cell. So this mutation may have a locational advantage of interfering with the immune system’s bid to prevent virus binding and fusion.
Says the COG-UK report: “Given the experimentally predicted and plausible… consequences of some of these mutations, their unknown effect when present in combination and the high growth rate of [the variant] in the U.K., this novel lineage requires urgent laboratory characterisation and enhanced genomic surveillance worldwide.”
The South Africa variant
Is this new UK-variant related to the newly emergent variant in South Africa? The variant seems to have emerged in a major South African metropolitan area and was first detected in October. In its press statement of December 18, the South African Health Minister stated that a particular variant had increasingly dominated the findings of samples collected in the past two months. In addition, the statement said that there was evidence of a shift in the clinical epidemiological picture; in particular, a larger proportion of younger patients with no comorbidities were presenting with critical illness. The Minister also claimed that it was South Africa which alerted the U.K. authorities about the new variant which triggered the discovery of the U.K-variant.
While the UK-variant seems to have only caused an increase in the number of cases among younger adults, there was no evidence of increase in severity of the disease in any age group. However, in the South African scenario severe illness was also being observed in young adults. “The evidence that has been collated,” he said, “strongly suggests that that the current second wave we are experiencing is being driven by this new variant.” The SA-variant too carries the same critical mutation N501Y, which, scientists believe, may be responsible for the increase in the virus’s greater infectiveness in both countries. Does this lead to severe disease in young adults? Only more studies on the variants can tell. The exact impact of its tighter binding to human ACE2 receptor is, however, not properly understood yet. However, according to Andrew Preston of the University of Bath, the mutation has been seen in other variants as well that have not been associated with increased transmission. “So, the picture is complex.”
Genetic analysis of the SA-variant has shown that it also has an unusually large number of mutations like the UK-variant. But the key mutation, N501Y, occurs in combination with other mutations that are not seen in the UK-variant. So, in all likelihood, it emerged completely independently of the U.K. strain and is not related to it. The SA-variant is characterised by N501Y, E484K and K417N mutations, two of them (N501Y and E484K) within the RBD, and the strain has been now called ‘501Y V2’.
Despite the above concerns in the behaviour of the two new variants from the U.K. and South Africa, scientists believe that there is no reason to think that the vaccines being rolled out or under development will be less effective. According to the Centres for Disease Control (CDC) of the U.S., the U.S. Food and Drug Administration (FDA) authorised vaccines are ‘polyclonal’; that is, they produce antibodies targeting several parts of the spike protein. The virus would likely need to accumulate several mutations in the spike protein to evade immunity induced by vaccines or by natural infection, the CDC says.
However, in a recent study by Paul Axelson and others from the University of Pennsylvania Perelman School of Medicine, which was posted on the bioRxiv web preprint repository on December 13, 16 naturally occurring mutations on the S-protein, including the N501Y mutation, were investigated to determine whether these were able to prevent antibody binding and maintain the ability to bind to the ACE2 receptor and viral infectivity.
Significantly, the authors concluded that “SARS-CoV-2 with mutated forms of the spike protein may retain the ability to bind to ACE2 while evading recognition by antibodies…. It seems likely that immune evasion will be possible regardless of whether the spike protein was encountered in the form of infectious virus, or as the immunogen in a vaccine. Therefore, it also seems likely that reinfection with a variant strain of SARS-CoV-2 may occur among people who recover from COVID-19, and that vaccines with the ability to generate antibodies against multiple variant forms of the spike protein will be necessary to protect against variant forms of SARS-CoV-2 that are already circulating in the human population” (emphasis added). Whether all vaccines already developed or under development are really of this nature is not known.
There are already several challenges that the rapid roll-out scenarios proposed for public use must confront (Table 1). The emergence of new uncertainties due to the somewhat unusual virus mutations seen during a pandemic adds another dimension. Among the various concerns about the impact of the new variants, the ability to evade vaccine-induced immunity would likely be the most concerning because once a large proportion of the population is vaccinated, there will be immune pressure that could favour and accelerate emergence of such variants by selecting for “escape mutants”. There is no evidence that this is occurring, and most experts believe escape mutants are unlikely to emerge because of the nature of the virus, says the CDC.
In the Indian context, the only viable vaccine currently is Oxford-AstraZeneca’s adenovirus vectored-vaccine, which is the most easily deliverable vaccine given its easily manageable cold chain logistics. Vaccination prospects in India are, therefore, currently dependent entirely on its British approval. Following that India is likely to approve for use here immediately. But the vaccine’s approval in the U.K., in the light of the emergence of this new variant and its rapid spread, may not come soon. The U.K. health authorities may want to see its efficacy against cases with the new variant(s) before. So, Indian roll-out plans should actually speed up trials and approvals for home-grown vaccines, but approvals must take into account all the new lessons being continually learnt from the virus variants’ infecting potential.