By Khalid Munir (PhD, DVM), PetLife Veterinary Professional Corporation, NJ, USA.
Isra Munir (BS, DMD Program), University of Pennsylvania, PA, USA.
Hamna Khalid (Chemical and Biological Engineering), Villanova University, PA, USA.
Isabella Verzberger (PhD, DVM), Population Health Research Institute, ON, Canada.
Zareen Fatima (PhD Virology), Pet Cancer Fund, Toronto, ON, Canada.
Usama Fraaz (BS, MD program), NOSM, Laurentian University, ON, Canada
Hammad Ahmed Hashmi (DVM, MSc, MBA, CMIT), DHA Kennel Club, Lahore.
Rukhsana Munir (MBBS, MCEM, FRCEM), Consultant Emergency Physician,
Russells Hall Hospital, Dudley, England, UK.
Noreen Mukhtar (BDS), PetLife Veterinary Professional Corporation, NJ, USA
Aysha Saeed (BSc, MBChB Medicine Program), University of Exeter, UK.
Fraaz Mahmood (BASc PH&S, DVM, MSc), Health Canada, ON, Canada.
Sohaib Ashraf, MBBS, Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, USA.
M Akram Muneer (DVM, PhD), Ripah International University, Lahore.
A new Coronavirus disease referred to as COVID-19 is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). This highly infectious disease was first reported to the World Health Organization (WHO) on December 31 2019. Since then, this virus has spread to almost all the countries worldwide, getting the status of a pandemic from WHO on March 11, 2020. SARS-CoV-2 continues to be a severe threat to the global economy and public health since its emergence from Wuhan, China, in early December 2019. Coronaviruses contain large RNA genomes with proof-reading ability; however, like other RNA viruses, they also acquire random mutations over time. As the virus goes through various evolutionary pathways, the new genotypes of the virus are emerging with multiple mutations in genes encoding the Spike (S) proteins, RNA polymerase, RNA primase, and nucleoprotein. The new SARS-CoV-2 genotypes (and the consequent change in the viral phenotypes) may have important implications not only for the molecular epidemiology and re-infections with variants but also for the vaccine development, immunization campaigns and whether or not the current available COVID-19 vaccines would hold and confer cross-protective immunity against these viral variants.
All RNA viruses naturally mutate over time, and SARS-CoV-2 is no exception. The vast majority of mutations in various viral genes are “passengers” and will have little impact, i.e., they do not change the virus’s biological behaviour and are just carried along. But every once in a while, a virus strain strikes lucky by mutating in a way that helps it survive and replicate more efficiently. Virus strain carrying these mutations can increase in frequency due to natural selection, given the right epidemiological settings. This is what seems to be happening with at least one or two SARS-CoV-2 variants identified so far. Scientists and researchers are working on sequencing the genomes (genetic material) of SARS-CoV-2 isolates from millions of cases. Since its first identification about a year ago, several hundreds of mutations have been detected in the genomes of SARS-CoV-2 isolates sequenced so far. Although the mutation rate in SARS-CoV-2 is less than that of influenza A viruses, this virus is acquiring approximately one to two mutations in its genome every month. Many mutations are silent and do not affect the function and structure of viral proteins. Some, however, may be non-silent and impact the structure and function of the viral protein(s). The critical concept among “corona-virologists” is that human coronaviruses are non-pathogenic in their natural reservoir hosts but become pathogenic after their transmission to a new host species. With further evolution, the viruses adapt to the new host and become more transmissible and less pathogenic or virulent. Virulence is the disease-producing power of the virus, whereas pathogenicity is the virus’s potential ability to produce disease in the susceptible host population. Therefore, it is possible that a progenitor of SARS-CoV-2 jumped from bats through pangolins and perhaps another unknown intermediate host into humans and adapted from the more virulent and pathogenic strain to a more transmissible viral strain responsible for the current pandemic. This is an essential strategy for viruses to keep increasing their copy number. It is interesting to note that SARS-CoV-2 shows less pathogenicity than SARS-CoV-1 (the cause of Severe Acute Respiratory Syndrome, SARS) and MERS-CoV (responsible for causing Middle Eastern Respiratory Syndrome, MERS). Viruses such as SARS-CoV-2 aim to attain a point of equilibrium with their host(s) and become endemic without causing high mortality in the susceptible host population. SARS-CoV-2 in humans is likely to continue evolving on these lines and become adapted further to humans to become less pathogenic or virulent.
The UK variant, known as VOC 202012/01 of lineage B117, has been spreading rapidly in London and the UK’s southeastern region since September of 2020. The UK variant has accounted for more than 60% of the London area’s recent infections, and its presence has been reported in more than 50 countries of the world, including the US, Canada and Pakistan. The presence of a similar but new variant, 20H/501Y.V2 of lineage B1351, has also been confirmed in South Africa. The UK and South African virus variants have changes in the spike gene consistent with the possibility that they are more infectious. There is a particular concern about the South African variant, which has several S protein changes, and scientists do not know their ramifications. Early epidemiological data and calculated R0 value (the primary reproductive number) connect the UK variant with higher transmission rates, i.e., spreading more quickly among humans than the South African variant and other previously identified strain(s). However, there have been no links between this new variant and enhanced virulence/ pathogenicity in humans. An important point to note is how might the B117 lineage variant have evolved? Scientists believe it acquired its mutations in a single immunocompromised patient. In such patients, the virus remains mutating for months, and when the patients are treated with convalescent plasma, it may put selection pressure on the mutating strains. They may escape the attack quickly, hence, spreading the infectious virus to other people.
The current knowledge provides some insight into the mutational spectrum of the UK variant. The projections based on computational structural modelling, considering the mutations associated with the viral S protein and its receptor-binding domain (RBD), have several important implications:
- The mutation at 501 amino acid of asparagine to tyrosine (N501Y) in the UK variant may lead to more effective RBD binding of the S protein angiotensin-converting enzyme (ACE2) receptor on host cells.
- The mutation near the furin cleavage site of the Spike protein may lead to a conformational change in the Spike protein leading to higher infectivity of the virus. These mutation-induced enhanced functions may increase the transmissibility of SARS-COV-2 variants, i.e., increased and rapid capacity to spread among humans. They may also change the virus’s ability to cause disease among humans either positively or negatively, i.e., may result in a silent infection, a milder or more severe disease.
- These mutations may give the variant the ability to evade vaccine-induced immune responses.
The consequence of such immune evasion could be potentially devastating as the population starts to get vaccinated and builds immunity, which the emergence of “escape mutants could theoretically destroy”. However, mutations in the S protein of the UK variant account for about one per cent of amino acid sequence change; hence viral evasion of the vaccine-induced immunity is less likely because antibody-mediated immunity produced by the COVID-19 vaccines approved so far would be polyclonal. Polyclonal antibodies are a heterogeneous mixture, which is usually made by different B lymphocyte-clones in the body. They can recognize and bind to many different epitopes (part of an antigen molecule to which an antibody attaches) present on a single antigen. In other words, antibodies target various epitopes on the S protein of SARS-CoV-2.
Additionally, the local (mucosal) immunity and the cell-mediated component of the adaptive immune responses would also play a role in conferring protective immunity to individuals vaccinated against SARS-CoV-2. Fourth, mutations may make the variant less prone to therapy with specific monoclonal antibodies. Finally, the variant strain may not be accurately detectable by the diagnostic tests developed explicitly for the parental or original SARS-CoV-2 strain. According to the US Food and Drug Administration, the deletions at 69-70 amino acids in B117 lineage may appear to affect the molecular detection of SARS CoV-2 by a few diagnostic kits. Presently, it is not conclusively known how significantly these mutations affect the clinical or epidemiological manifestations of COVID-19. The projections based on structural modelling require confirmation through further studies in humans or animal models.
The South African variant contains multiple S protein mutations, including K417T, E484K, N501. According to a recent report, E484K may affect virus neutralization by some polyclonal or monoclonal antibodies. However, further confirmation is required through in-vivo experiments in humans and animal models. In Brazil, another variant of SARS-CoV-2, known as P1, has emerged; this variant was identified in individuals travelling from Brazil to Tokyo, Japan. This variant has 17 unique mutations, including three in the RBD of the S protein. The three mutations in the S protein RBD are K417T, E484K, and N501Y. A piece of limited evidence suggests that some of these mutations in the P.1 variant may affect its transmissibility and antigenic nature, which in turn may affect the ability of pre-existing or vaccine-induced antibodies to recognize and neutralize this variant virus. This variant’s emergence raises concerns for a potential increase in transmissibility or susceptibility of recovered individuals to re-infection with a new variant of SARS-CoV-2. Very recently (on January 18, 2021), the presence of yet another SARS-CoV-2 variant, known as L452R, was reported by the California Department of Public Health in the US; this variant carries three mutations, including the ones in the spike protein. Identifying these SARS-CoV-2 variants in different countries of the world has raised the concern that they may be vaccine-resistant. In the immediate future, with the vaccine drive in place and more vaccine approvals on the way, it is essential to achieve immunity quickly in 70% of the population (herd immunity) to help control the escape mutants. With immunization on the way and the complex, healthy body immune mechanisms, no matter how the virus twists and weaves, given the diversity and enormously different antibody specificities, and not to mention the other innate and adaptive immune responses of the host population, it is not easy for SARS-CoV-2 to escape the body’s defence mechanisms, despite the many variations it may adopt. The optimistic outcome would be that the mRNA vaccines would generate not only the humoral immune responses but also cytotoxic T-cells activation and differentiation, and these massive immune responses together, all of which are typically not activated with the conventional vaccines, would be able to fight SARS-CoV-2 and its “mild” variants.
Several other genotypes, antigenic variants and pathotypes of SARS-CoV-2 may be circulating in the field. The characterization of mutations in various viral genes is essential not only for revealing the predominant mutant in an epidemic (molecular epidemiology) but also for monitoring and tracking the outbreak of infectious pathogens as well as understanding the viral drug resistance, immune evasion, and disease development mechanisms, effective vaccine development, antiviral drugs, and diagnostic assays. Thus, more research is needed to decisively link the genetic makeup of different strains/ variants of the virus with the severity and presentation of disease in patients infected with SARS-CoV-2 and fathom differences in transmissibility virulence caused by mutations in various SARS-CoV-2 genes. The type of modifications in SARS-CoV-2 that allow for human infection and transmission and the impact of these viral mutations on specific vaccines’ long-term efficacy requires further investigations. Moreover, the virus’s relatively rapid changing genetic makeup may limit the effectiveness of newly developed vaccines over time. As more mutations emerge in SARS-CoV-2 over time, the COVID-19 vaccines may need to be updated to match them with the circulating field strain. This also happens with seasonal flu or influenza virus in the UK and USA, and some other countries; this virus accumulates mutations throughout the year. The antigen in the flu vaccine is adjusted accordingly every year or so. It is also possible polyvalent vaccines containing two or more antigenic variants of SARS-CoV-2 may need to be developed in the long term.
