Since neither D614G nor N439K has shown the ability to increase the severity of the disease or to escape from neutralizing antibodies, the genetic lineages with these mutations are not classified as VOC. However, the variants of VOC are characterized by RBD mutations, which in turn alter the ACE2 interaction, and diminish the neutralizing antibodies activity.
The most discussed VOC in academic literature and media are Alpha (lineage B.1.1.7), Beta (lineage B.1.351), Gamma (lineage P.1), and Delta (lineage B.1.617.2) and initially found in United Kingdom, South Africa, Brazilia, and India, respectively. The B.1.1.7 lineage was discovered in Kent (UK) in late 2020. There are 23 mutations in the genome B.1.1.7, including a mutation in RBD N501Y, which increases the affinity of binding ACE2 receptor [26]. The spread of the B.1.1.7 lineage was insufficiently constrained by the UK-enforced anti-epidemic measures compared to other genetic variants [27], probably due to a higher basic reproductive number (R0) that increased from 0.4 to 0.7 [28]. There is evidence that B.1.1.7 variants increased lethality [29] and moderate escape from the antibody-neutralizing effects [30,31,32]. This lineage is already dominant in the UK and is widely spread throughout Europe and the United States [28,33,34].
The VNA against B.1.1.7 variant showed 2.1-fold reduction for the AstraZeneca ChAdOx1 nCoV-19 vaccine after 28 days following the second dose compared to SARS-CoV-2 Victoria strain. In a similar study sera VNA levels induced with the Pfizer-BioNTech vaccine BNT162b2 were reduced by 3.3 times [32]. In another study, AstraZeneca vaccine showed nine times VNA reduction in a live virus assay, while the epidemiological decrease of vaccine efficacy was insignificant (not exceeding 11%) [35].
The first case of B.1.1.7 in Russia was officially registered on January 10, 2021, reaching the frequency of 17.4% in March 2021 [36]. In our study, the decrease in VNA efficacy against B.1.1.7 variant for sera of people vaccinated with Sputnik V in both live virus (Figure 3) and Spike-pseudotyped lentiviruses assays (Figure S4) was statistically insignificant. These results demonstrate the high efficacy of the Sputnik V vaccine against the UK variant B.1.1.7, which is actively spreading in Europe, America, and, putatively, Russia.
Recently emerged Delta variant B.1.617 seems to be polymorphic and consists of B.1.617.1, B.1.617.2, and B.1.617.3 [9]. Among these variants B.1.617.2 only has VOC status (VOC-21APR-02). We isolated two variants B.1.617.2 (S: T19R G142D E156G F157del R158del L452R T478K D614G P681R D950N) and B.1.617.3 (S: T19R G142D E156G F157del R158del L452R E484Q D614G P681R D950N). Two mutations of RBD including T478K and E484Q differentiate these variants from each other. Our study reveals that antibody evasion of B.1.617.2 (2.5 VNT decrease) may contribute to the rapid spread of this variant in India and around the world.
The B.1.351 lineage is of much greater concern [37]. This lineage was discovered in South Africa during the first pandemic wave in the heavily affected metropolis (Nelson Mandela Bay) located on the coast of the Eastern Cape province. This genetic lineage spread rapidly and became dominant in the Eastern Cape, Western Cape, and KwaZulu-Natal provinces within several weeks. The available genomic data indicate the rapid spread of this lineage and the displacement of other virus lineages in several regions. This lineage is characterized by eight mutations in S protein, including three substitutions in the RBD (K417N, E484K, and N501Y) resulting in increased transmissibility [37] and immune escape [38]. The separate contribution of these individual mutations was already described [39,40]. Specifically, N501Y is a well-known mutation of the UK strain B.1.1.7 that can increase interaction with ACE2 and contribute to the partial escape from the neutralizing effect of antibodies. For the K417N mutation, a positive effect on the interaction with ACE2 and a weakened interaction with the neutralizing antibody STE90-C11 were shown [40]. The K417N mutation shows a more pronounced effect in combination with N501Y [40] further amplified by the E484K mutation [41,42]. The E484K mutation is currently found in VOC B.1.351, P.1, P.2, and in the newly emerged Alpha strain B.1.1.7 with an additional E484K mutation. A comparative study showed a 20- and 40-fold decrease in viral-neutralizing activity against B.1.351 by sera obtained from the people vaccinated with Moderna/mRNA-1273 and Pfizer/BNT162b2 vaccines, respectively [14]. In the cases of P.1 widely spread in Latin America and Southeast Asia, the reduction in serum neutralization is 4.5 for Moderna/mRNA-1273 and 6.7 for Pfizer/BNT162b2, respectively.
In our study, a three-fold decrease in the viral-neutralizing activity of B.1.351 variant was recorded for sera of the patients vaccinated with Sputnik V for Spike-pseudotyped lentivirus (Figure S4) and a 3.1-fold decrease for a live viral isolate (Figure 3), 2.8-fold decrease was recorded for P.1 variant. The decreased neutralization effect is observed most prominently for weakly reactive serums. Thus, maintaining high titers of antibodies as a result of Sputnik V vaccination or subsequent revaccinations can be one of the solutions to provide high virus-neutralizing activity against VOC B.1.351, P.1, B.1.617.2, and other emerging variants. The results obtained in the current study for Sputnik V compare favorably with the results of other prophylactic vaccines, although direct comparisons are not possible due to the absence of the unified methodology for assessing the virus-neutralizing effect. Single cases of local B.1.351 variant transmissions have been reported in Russia since March 16 [43]. It is noteworthy that, except for B.1.351 has not yet become widespread on other continents, and only imported cases and isolated local transmissions are currently recorded [44]. It is not clear to what extent we can expect this lineage to spread along other continents. The low incidence rate can be attributed both to the insufficient time that has elapsed since the emergence of the B.1.351 lineage, and/or the difficulty of this lineage competing with those already circulating in other continents. It is possible that the competitive advantage can only fully manifest itself after achieving a high percentage of immune people, considering the efficacy at which B.1.351 escapes the neutralizing immune response.
The epidemiologic efficacy of AstraZeneca ChAdOx1 nCoV-19 vaccine against B.1.351 variant was only 10.4% (95% CI, −76.8 to 54.
[44,45]. It is worth noting that this efficacy is specified for mild to moderate cases of the disease. The protective efficacy of ChAdOx1 nCoV-19 against severe disease is currently unknown. For Novovax recombinant vaccine and Janssen adenovirus vaccine, the epidemiological efficacy in South Africa, where genotype B 1.351 is dominant, was 60% and 57%, respectively [38]. The records for the Janssen vaccine were mostly made for severe disease cases. Probably, most of the vaccines will reduce the preventive effect in the cases of mild disease, though they will retain the preventive effect against cases of severe disease. The problems of recording methodology do not allow for direct comparisons of the epidemiological vaccine performance.
It becomes obvious that under conditions of increasing herd immunity developed as a result of the past disease and vaccination, the number of SARS-CoV-2 variants with mutations in RBD and S protein will rapidly increase. Some of the mutation variants occur independently in different genetic lineages, i.e., N439K [25] or the E484K mutation [9]. In our study, in addition to the emergence of expected VOC in Russia, we studied the diversity of local genetic lineages with mutations in the RBD. A significant percentage of the substitution variants that are becoming common is recorded: S477N + A522S (27.8%), N501Y (4.73%), E484K (3.55%), T385I (2.37%), E484K + S494P (1.77%), N439K (1.18%), Y508H (0.59%), T478K (0.59%), S477N (0.59%), N501T (0.59%). These data are in concordance with previously reported analysis for Russia where S477N, A522S, T385I, and E484K mutation rates were found extensively increasing according to GISAID [10]. All these mutations were already reported as increasing the affinity for ACE2 receptor and/or decreasing the antibody-neutralizing effect (Table S1). We assessed the virus-neutralizing effect of serum in the patients vaccinated with Sputnik V based on live virus isolates, which showed a non-significant decrease in the antibody-neutralizing effect against B.1.1.397 (T385I) and B.1.1.317 (S477N, A522S).
Virus-neutralizing activity assay protocol used in the current study was previously validated in 1–3 phases of the Sputnik V vaccine clinical trials thus making it possible to directly compare the obtained results with the previous data [1,18].
The virus-neutralizing serum activity is a dynamic parameter. Booster immunization with a second dose is used to increase the number of antibodies and prolong their protective period of action. In case of the Sputnik V, a heterologous prime-booster scheme implementing different vector adenoviruses allows the use of a booster dose as soon as 21 days after the first immunization. In this case, antibodies formed against the adenovirus carrier do not interfere with the boosting effect.
Summarizing the obtained data, we can conclude that for the B.1.1.7, B.1.617.3, and local Moscow variants of genetic lineages B.1.1.141 (T385I) and B.1.1.317 (S477N, A522S) neutralizing properties of Sputnik V induced sera are not changed. For the B.1.351, P.1, and B.1.617.2 VOCs statistically significant 3.1-, 2.8-, and 2.5-fold, respectively, VNA reduction was observed. Notably decrease in VNT to VOC (B.1.351, P.1, B.1.617.2) in Sputnik V vaccinated sera is not as significant as for other vaccines described above. However, in order to make a final conclusion, it is necessary to conduct a direct comparative study. The decreased neutralization effect is of concern and requires further surveillance and epidemiological studies.
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