SARS-CoV-2 mutations similar to those in the B1.1.7 UK variant could arise in cases of chronic infection, where treatment over an extended period can provide the virus multiple opportunities to evolve, say scientists.
Writing in Nature, a team led by Cambridge researchers report how they were able to observe SARS-CoV-2 mutating in the case of an immunocompromised patient treated with convalescent plasma.
In particular, they saw the emergence of a key mutation also seen in the new variant that led to the UK being forced once again into strict lockdown, though there is no suggestion that the variant originated from this patient.
Using a synthetic version of the virus Spike protein created in the lab, the team showed that specific changes to its genetic code – the mutation seen in the B1.1.7 variant – made the virus twice as infectious on cells as the more common strain.
SARS-CoV-2, the virus that causes COVID-19, is a betacoronavirus. Its RNA – its genetic code – is comprised of a series of nucleotides (chemical structures represented by the letters A, C, G and U).
As the virus replicates itself, this code can be mis-transcribed, leading to errors, known as mutations. Coronaviruses have a relatively modest mutation rate at around 23 nucleotide substitutions per year.
Of particular concern are mutations that might change the structure of the ‘spike protein’, which sits on the surface of the virus, giving it its characteristic crown-like shape. The virus uses this protein to attach to the ACE2 receptor on the surface of the host’s cells, allowing it entry into the cells where it hijacks their machinery to allow it to replicate and spread throughout the body. Most of the current vaccines in use or being trialed target the spike protein and there is concern that mutations may affect the efficacy of these vaccines.
UK researchers within the Cambridge-led COVID-19 Genomics UK (COG-UK) Consortium have identified a particular variant of the virus that includes important changes that appear to make it more infectious: the ΔH69/ΔV70 amino acid deletion in part of the spike protein is one of the key changes in this variant.
Although the ΔH69/ΔV70 deletion has been detected multiple times, until now, scientists had not seen them emerge within an individual. However, in a study published today in Nature, Cambridge researchers document how these mutations appeared in a COVID-19 patient admitted to Addenbrooke’s Hospital, part of Cambridge University Hospitals NHS Foundation Trust.
The individual concerned was a man in his seventies who had previously been diagnosed with marginal B cell lymphoma and had recently received chemotherapy, meaning that that his immune system was seriously compromised.
After admission, the patient was provided with a number of treatments, including the antiviral drug remdesivir and convalescent plasma – that is, plasma containing antibodies taken from the blood of a patient who had successfully cleared the virus from their system. Despite his condition initially stabilizing, he later began to deteriorate.
He was admitted to the intensive care unit and received further treatment, but later died.
During the patient’s stay, 23 viral samples were available for analysis, the majority from his nose and throat. These were sequenced as part of COG-UK. It was in these sequences that the researchers observed the virus’s genome mutating.
Between days 66 and 82, following the first two administrations of convalescent sera, the team observed a dramatic shift in the virus population, with a variant bearing ΔH69/ΔV70 deletions, alongside a mutation in the spike protein known as D796H, becoming dominant. Although this variant initially appeared to die away, it re-emerged again when the third course of remdesivir and convalescent plasma therapy were administered.
Professor Ravi Gupta from the Cambridge Institute of Therapeutic Immunology & Infectious Disease, who led the research, said: “What we were seeing was essentially a competition between different variants of the virus, and we think it was driven by the convalescent plasma therapy.
“The virus that eventually won out – which had the D796H mutation and ΔH69/ΔV70 deletions – initially gained the upper hand during convalescent plasma therapy before being overtaken by other strains, but re-emerged when the therapy was resumed. One of the mutations is in the new UK variant, though there is no suggestion that our patient was where they first arose.”
Under strictly-controlled conditions, the researchers created and tested a synthetic version of the virus with the ΔH69/ΔV70 deletions and D796H mutations both individually and together. The combined mutations made the virus less sensitive to neutralization by convalescent plasma, though it appears that the D796H mutation alone was responsible for the reduction in susceptibility to the antibodies in the plasma.
The D796H mutation alone led to a loss of infection in absence of plasma, typical of mutations that viruses acquire in order to escape from immune pressure.
The researchers found that the ΔH69/ΔV70 deletion by itself made the virus twice as infectious as the previously dominant variant. The researchers believe the role of the deletion was to compensate for the loss of infectiousness due to the D796H mutation. This paradigm is classic for viruses, whereby escape mutations are followed by or accompanied by compensatory mutations.
“Given that both vaccines and therapeutics are aimed at the spike protein, which we saw mutate in our patient, our study raises the worrying possibility that the virus could mutate to outwit our vaccines,” added Professor Gupta.
“This effect is unlikely to occur in patients with functioning immune systems, where viral diversity is likely to be lower due to better immune control. But it highlights the care we need to take when treating immunocompromised patients, where prolonged viral replication can occur, giving greater opportunity for the virus to mutate.”
Multiple SARS-CoV-2 variants are circulating globally. Several new variants emerged in the fall of 2020, most notably:
- In the United Kingdom (UK), a new variant of SARS-CoV-2 (known as 20I/501Y.V1, VOC 202012/01, or B.1.1.7) emerged with a large number of mutations. This variant has since been detected in numerous countries around the world, including the United States (US). In January 2021, scientists from UK reported evidence that suggests the B.1.1.7 variant may be associated with an increased risk of death compared with other variants. More studies are needed to confirm this finding. This variant was reported in the US at the end of December 2020.
- In South Africa, another variant of SARS-CoV-2 (known as 20H/501Y.V2 or B.1.351) emerged independently of B.1.1.7. This variant shares some mutations with B.1.1.7. Cases attributed to this variant have been detected in multiple countries outside of South Africa. This variant was reported in the US at the end of January 2021.
- In Brazil, a variant of SARS-CoV-2 (known as P.1) emerged that was first was identified in four travelers from Brazil, who were tested during routine screening at Haneda airport outside Tokyo, Japan. This variant has 17 unique mutations, including three in the receptor binding domain of the spike protein. This variant was detected in the US at the end of January 2021.
Scientists are working to learn more about these variants to better understand how easily they might be transmitted and the effectiveness of currently authorized vaccines against them. New information about the virologic, epidemiologic, and clinical characteristics of these variants is rapidly emerging.
CDC, in collaboration with other public health agencies, is monitoring the situation closely. CDC is working to detect and characterize emerging viral variants. Furthermore, CDC has staff available to provide technical support to investigate the epidemiologic and clinical characteristics of SARS-CoV-2 variant infections. CDC will communicate new information as it becomes available.
B.1.1.7 lineage (a.k.a. 20I/501Y.V1 Variant of Concern (VOC) 202012/01)
- This variant has a mutation in the receptor binding domain (RBD) of the spike protein at position 501, where the amino acid asparagine (N) has been replaced with tyrosine (Y). The shorthand for this mutation is N501Y. This variant also has several other mutations, including:
- 69/70 deletion: occurred spontaneously many times and likely leads to a conformational change in the spike protein
- P681H: near the S1/S2 furin cleavage site, a site with high variability in coronaviruses. This mutation has also emerged spontaneously multiple times.
- This variant is estimated to have first emerged in the UK during September 2020.
- Since December 20, 2020, several countries have reported cases of the B.1.1.7 lineage, including the United States.
- This variant is associated with increased transmissibility (i.e., more efficient and rapid transmission).
- In January 2021, scientists from UK reported evidence that suggests the B.1.1.7 variant may be associated with an increased risk of death compared with other variants.
- Early reports found no evidence to suggest that the variant has any impact on the severity of disease or vaccine efficacy.,,
B.1.351 lineage (a.k.a. 20H/501Y.V2)
- This variant has multiple mutations in the spike protein, including K417N, E484K, N501Y. Unlike the B.1.1.7 lineage detected in the UK, this variant does not contain the deletion at 69/70.
- This variant was first identified in Nelson Mandela Bay, South Africa, in samples dating back to the beginning of October 2020, and cases have since been detected outside of South Africa, including the United States
- The variant also was identified in Zambia in late December 2020, at which time it appeared to be the predominant variant in the country.
- Currently there is no evidence to suggest that this variant has any impact on disease severity.
- There is some evidence to indicate that one of the spike protein mutations, E484K, may affect neutralization by some polyclonal and monoclonal antibodies.,
P.1 lineage (a.k.a. 20J/501Y.V3)
- The P.1 variant is a branch off the B.1.1.28 lineage that was first reported by the National Institute of Infectious Diseases (NIID) in Japan in four travelers from Brazil, sampled during routine screening at Haneda airport outside Tokyo.
- The P.1 lineage contains three mutations in the spike protein receptor binding domain: K417T, E484K, and N501Y.
- There is evidence to suggest that some of the mutations in the P.1 variant may affect its transmissibility and antigenic profile, which may affect the ability of antibodies generated through a previous natural infection or through vaccination to recognize and neutralize the virus.
- A recent study reported on a cluster of cases in Manaus, the largest city in the Amazon region, in which the P.1 variant was identified in 42% of the specimens sequenced from late December. In this region, it is estimated that approximately 75% of the population had been infected with SARS-CoV2 as of October 2020. However, since mid-December the region has observed a surge in cases. The emergence of this variant raises concerns of a potential increase in transmissibility or propensity for SARS-CoV-2 re-infection of individuals.
- This variant was identified in the United States at the end of January 2021.
Why Strain Surveillance is Important for Public Health
CDC has been conducting SARS-CoV-2 strain surveillance to build a collection of SARS-CoV-2 specimens and sequences to support public health response. Routine analysis of the available genetic sequence data will enable CDC and its public health partners to identify variant viruses for further characterization.
Viruses generally acquire mutations over time, giving rise to new variants. For instance, another variant recently emerged in Nigeria. CDC also is monitoring this strain but, at this time, it has shown no concerning characteristics to public health experts.
Some of the potential consequences of emerging variants are the following:
- Ability to spread more quickly in people. There is already evidence that one mutation, D614G, confers increased ability to spread more quickly than the wild-type SARS-CoV-2. In the laboratory, 614G variants propagate more quickly in human respiratory epithelial cells, outcompeting 614D viruses. There also is epidemiologic evidence that the 614G variant spreads more quickly than viruses without the mutation.
- Ability to cause either milder or more severe disease in people. In January 2021, experts in the UK reported that B.1.1.7 variant may be associated with an increased risk of death compared to other variants. More studies are needed to confirm this finding.
- Ability to evade detection by specific viral diagnostic tests. Most commercial reverse-transcription polymerase chain reaction (RT-PCR)-based tests have multiple targets to detect the virus, such that even if a mutation impacts one of the targets, the other RT-PCR targets will still work.
- Decreased susceptibility to therapeutic agents such as monoclonal antibodies.
- Ability to evade natural or vaccine-induced immunity. Both vaccination against and natural infection with SARS-CoV-2 produce a “polyclonal” response that targets several parts of the spike protein. The virus would likely need to accumulate multiple mutations in the spike protein to evade immunity induced by vaccines or by natural infection.
Among these possibilities, the last—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 favor 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.
 Analysis of sequences from the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Nigeria, identified two SARS-CoV-2 sequences belonging to the B.1.1.207 lineage. These sequences share one non-synonymous mutation in the spike protein (P681H) in common with the B.1.1.7 lineage but does not share any of the other 22 unique mutations of B.1.1.7 lineage. The P681H residue is near the S1/S2 furin cleavage site, a site with high variability in coronaviruses. At this time, it is unknown when this variant may have first emerged. Currently there is no evidence to indicate this variant has any impact on disease severity or is contributing to increased transmission of SARS-CoV-2 in Nigeria.
 “Wild-type” refers to the strain of virus – or background strain – that contains no major mutations.
Strain Surveillance in the US
In the United States, sequence-based strain surveillance has been ramping up with the following components:
- National SARS-CoV-2 Strain Surveillance (“NS3”): Since November 2020, state health departments and other public health agencies have been regularly sending SARS-CoV-2 samples to CDC for sequencing and further characterization. This system is now being scaled to process 750 samples nationally per week. One strength of this system is that it allows for characterization of viruses beyond what sequencing alone can provide.
- Surveillance in partnership with commercial diagnostic laboratories: CDC is contracting with large national reference labs to provide sequence data from across the United States. As of mid-January, CDC has commitments from these laboratories to sequence 6,000 samples per week and is exploring options to increase this number.
- Contracts with universities: CDC has contracts with seven universities to conduct genomic surveillance in collaboration with public health agencies.
- Sequencing within state and local health departments: Since 2014, CDC’s Advanced Molecular Detection Program has been integrating next-generation sequencing and bioinformatics capabilities into the US public health system. Several state and local health departments have been applying these resources as part of their response to COVID-19. To further support these efforts, CDC released $15 million in funding, with COVID supplemental funds, through the Epidemiology and Laboratory Capacity Program on December 18, 2020.
- The SPHERES consortium: Since early in the pandemic, CDC has led a national consortium of laboratories sequencing SARS-CoV-2 (SPHERES) to coordinate US sequencing efforts outside of CDC. The SPHERES consortium consists of more than 160 institutions, including academic centers, industry, non-governmental organizations, and public health agencies.
Through these efforts, anonymous genomic data are made available through public databases for use by public health professionals, researchers, and industry.
Horby P, Huntley C, Davies N, et al. NERVTAG note on B.1.1.7 severitypdf iconexternal icon. SAGE meeting report. January 21, 2021.
Wu K, Werner AP, Moliva JI, et al. mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants.external icon bioRxiv. Posted January 25, 2021.
Xie X, Zou J, Fontes-Garfias CR, et al. Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited seraexternal icon. bioRxiv. Posted January 7, 2021. Greaney AJ, Loes AN, Crawford KHD, et al. Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodiesexternal icon. bioRxiv. [Preprint posted online January 4, 2021]
Weisblum Y, Schmidt F, Zhang F, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variantsexternal iconexternal icon. eLife 2020;9:e61312.
Resende PC, Bezerra JF, de Vasconcelos RHT, at al. Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020external icon. [Posted on www.virological.orgexternal icon on January 10, 2021]
More information: Kemp, SA et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature; 5 Feb; DOI: 10.1038/s41586-021-03291-y