New progress of novel COVID-19 variants and its effect on vaccine immune protection

Cai-Hong Wang, Rong Wang, Yu-Xia Zhou, Xiao-Wen Yao, Xiao-Hui Yu, Jiu-CongZhang,3?

1.Department of Gastroenterology, The 940 Hospital of Joint Logistic Support Force of PLA, Lanzhou 730050, China

2.Gansu University of Traditional Chinese Medicine, Lanzhou 730000, China

3.The Sixth Division of Infectious Diseases, Huoshenshan Hospital, Wuhan 430050, China

ABSTRACT The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) poses a serious threat to human life and health as well as social and economic development. In order to deal with this public health event, scientific research institutions around the world have rapidly developed and put vaccines into urgent use, bringing hope to the victory over the epidemic. However, as the Novel Coronavirus continues to spread throughout the world, the virus genome has mutated to form a variety of variants. Among them, the Alpha,Beta, Gamma, Delta and Omicron variants show higher infectivity and higher resistance to vaccines and neutralizing antibodies, posing new challenges to the prevention and treatment of COVID-19. At present, the effect of variants on the effectiveness of developed vaccines has become a hot topic of global discussion. In this paper, we briefly review the new progress of novel Coronavirus variants and their effects on vaccine immune protection.

Keywords:COVID-19 Variants Vaccine Immune protection Review

The pneumonia caused by COVID-19 has caused a global public health emergency. Subsequently, on 11 February 2020, The World Health Organization (WHO) named the disease caused by this virus COVID[1]. On the same day, the International Committee on Virology named the novel coronavirus as Severe Acute Respiratory syndrome Coronavirus 2 (SARS-CoV-2)[2]. According to WHO statistics, As of January 7, 2022, more than 298 million people around the world were infected with SARS-CoV-2, resulting in more than 5.46 million deaths[3]. It is a serious threat to human life and health as well as social and economic development. In the absence of specific drug treatments, vaccines are the most effective means of containing a global pandemic. Of the 322 vaccine candidates proposed to date, 99 are in clinical trials, 25 have reached phase III efficacy studies and 18 have been approved, In particular,Pfizer-BNT162B2, Moderna-BNT162B2, Oxford AS-AZD-1222,Johnson ＆ Johnson AD26.COV2-S, Novavax NVX-COV2373 and other COVID-19 vaccines have brought hope to the victory over the epidemic[4]. However, As the Novel Coronavirus continues to spread throughout the world, The virus genome has mutated to form a variety of variants. Among them, the Alpha, Beta, Gamma, Delta and Omicron variants show higher infectivity and higher resistance to vaccines and neutralizing antibodies, posing new challenges to the prevention and treatment of COVID-19. At present, the effect of mutant strains on the effectiveness of developed vaccines has become a hot topic of global discussion. In this paper, we briefly review the new progress of novel Coronavirus variants and their effects on vaccine immune protection.

1. Structural characteristics of SARS-COV-2

SARS-CoV-2 is a single stranded righteous RNA virus with an envelope,belongingto theβcoronavirus family. Its genome size is about 29.9KB, and it has about 78%sequence homology with SARS-CoV[5]. Genomic RNA has two major open reading frames (ORFs),ORF1a and ORF1b, of which two thirds of the genome is translated into PP1A and PP1B proteins. One third of the genome has overlapping ORF encoding four main structural proteins, including spike protein (S protein),nucleocapsidprotein (N protein),membrane protein ( M protein),Envelope protein (E protein)and some helperproteins,etc. S protein is a kind of transmembrane protein composed of signal peptide(SP),receptor-binding domain(RBD),fusion peptide (FP) and S2 subunit of S1 subunit,which is the portal for virus to invade host cells. Among them,theN-terminal domain (NTD) of S1 subunit of S protein contributes to virus attachment, and S2 subunit mediates virus in c-terminal domain[6].The presence of an amino acid-rich alkaline furan cleavage site (S2')on the cleavage of S1 and S2 subunits,which acts asa fusion peptide during viral endocytosis, is a distinguishing feature of SARS-CoV-2,differentiating it from other viruses in origin.

Due to the remarkable similarity in RBD between SARS-CoV-2 and SARS, bothviruses exhibit binding mechanisms similar to the Human host cell receptor (ACE2).However,the significant characteristics of S2 'locus enhance the pathogenicity and transmissibility of SARS-CoV-2[7].The E protein, along with M and N proteins,promotes the formation of virus-like particles,while the S protein RBD binds to ACE2on the cell surface and becomes a core target for vaccine design[8].

2. Correlation of vaccine immunological protection

A vaccine is a biological agent that provides acquired immunity against a specificinfectious disease. This is done by activating lymphocytes with receptors specific to aparticular pathogenic microorganism, its toxin,or one of its surface proteins.Vaccinationworks by inducing humoral and cellular responses.The protective mechanisms of the COVID-19 vaccine are not fully understood. However, vaccine-induced neutralizing antibodies against SARS-CoV-2 S protein RBD are generally considered to be an important protective mechanism.One animal study showed that neutralizing antibodies against protein S provided near-complete protection against reinfection[9].Recent modeling studies have shown thatneutralizing antibody levels are highly predictive of protection against infection or severe disease[10]. A second modeling study showed a close correlation between neutralizing antibody levels and efficacy reported in trials of several COVID-19 vaccines[11].Athird efficacy trial study showed that titers of both binding and neutralizing antibodieswere associated with protective effects[12].

3. The impact of different COVID-19 variants on vaccines

In the early days of the COVID-19 pandemic, the number of"mutated" variants of the virus was low due to the low number of people infected with the virus. Later,with the increase of the number of infected people,it led to the evolution of a varietyof SARS-COV-2 variants and the emergence of a variety of mutant strains. However, the five variants of VOC (Variant of Concern)are the most widely reported: B.1.1.7, B.1.351, P.1, B.1.617.2,B.1.1.529variants with increased infectivity, increased virulenceand named vaccines and neutralizing resistance in Latin letters, They were Alpha,Beta,Gamma,Delta,And Omicron variants[13]. Compared with the Wuhan reference strain,The S protein of these variants was mainly changed.The rapid evolution and high frequency mutation of S protein may change the amino acid sequence of neutralizing antibody epitope, and then reduce its sensitivity to neutralizingantibody, and further affect the effectiveness of neutralizing antibody and vaccine.

3.1 Alpha (B.1.1.7) variant

B.1.1.7 was first discovered in The UK in September 2020,and it spread rapidly around the worldand, its infectivity was70% higher than that of D614G. B.1.1.7 Therewere 8 mutations in S protein of mutant strain (δ 69-70 deletion,δ 144 deletion,N501Y,A570D, P681H,T716I, S982A, D1118H)[14]. Therefore, currently available COVID-19 vaccines may not be effective against the B.1.1.7 lineage.Xie et al[15],By immunizing 20 participants with Pfizer vaccine BNT162b2 in serum.found that the virus carrying B.1.1.7 and B.1.351 variants shared the mutant N501Y and the N501 virus without the mutant strain had quite neutralizing activity.Muik et al[16],The study also showed that the neutralization efficacy of the immune serum produced by inoculation with Pfizer vaccine BNT162b2 against the Wuhan reference strain and B.1.1.7 pseudovirus remained basically unchanged overall.Wu et al[17],The results showed that the neutralization titer of Moderna vaccine Moderna mRNA-1273 against B.1.351 and P.1 variants decreased,but there was still a degree of neutralization ability, but there was no significant decrease in the neutralization titer against B.1.1.7 variants.

Emary et al[18],The study showed that the serum immunized with Oxford-Astrazeneca vaccine AZD1222 had a low titer of neutralizing antibodies against the B.1.1.7 lineage, but the response rate against the B.1.1.7 variant was 70. 4%.In animal studies[19], The neutralizing titer of oxford-Astrazeneca vaccine AZD1222 was not decreased or only slightly decreased against the B.1.1.7 variant, while the neutralizing antibody titer was decreased by a factor of 9 against the B.1.351 variant. Sadoff et al[20] showed that the serum produced by immunization with Johnson ＆ Johnson vaccine AD26.coV2-S could neutralize the B.1.1.7 variant strain in vitro, but the efficiency was lower than that of wuhan reference strain. Novavax demonstrated[21]in a Phase III clinical trial that its COVID-19 vaccine nvX-CoV2373 was 85% effective against the B.1.1.7 variant, 96% effective against the original strain, and less than 50% effective against B.1.351. So far, Pfizer, Oxford-Astrazeneca and Novavax vaccines have shown some protection against the B.1.1.7 variant.

3.2 Beta (B.1.351) variant

The B.1.351 variant was first identified in South Africa in May 2020 and is about 25% more transmissible than the previous epidemic strain.In addition, young people with comorbidities are more likely to be infected with this variant and more likely to cause severe illness than other variants. There were 9 mutations in S protein of mutant strain B.1.351 (L18F, D80A, D215G, R246I, K417N,E484K, N501Y, D614G and A701V). There are three mutations(N501Y, K417N and E484K) in the S-protein-based RBD. E484K is located in RBM and directly contacts specific ACE2 residues, which reduces the neutralization sensitivity to convalescence serum.

Wibmer et al[22]. compared the neutralization effect of monoclonal antibody and serum in recovery period of mutant B.1.351 with wuhan D614G mutation by using the neutralization test of spike pseudolentivirus, and the results showed that 48% of neutralizing antibodies did not detect the neutralization activity. In the nested pseudoviruses containing only RBD region mutations (K417N,E484K, N501Y), 27% of neutralizing antibodies were not detected,suggesting that the protective effect of current vaccines based on S protein may be affected. Liu et al[23]. Study showed that although K417N site does not bind to ACE2, it is an epitope of neutralizing antibody like E484K, so immune escape may also occur through K417N. The K417N and E484K mutations in B.1.351 significantly affected the neutralization of monoclonal antibodies and immune sera from patients in the recovery stage, and the neutralization titer in the serum of patients recovering from B.1.351 was 13.3 times lower on average than that of the early infected strain[24]. Wang et al[25]. also analyzed the serum test of 20 participants at the eighth week after they were vaccinated with Moderna vaccine mrNa-1273 and Pfizer vaccine BNT162b2, and the results showed that the neutralization activity of pseudoviruses containing E484K and N501Y mutations or the triple combination of K417N, E484K and N501Y decreased. Meanwhile, It was also found that the neutralization activity of monoclonal antibodies and immune sera against this variant was decreased due to the K417N and E484K mutations in B.1.351.

Johnson's ENSEMBLE trial demonstrated[26] an overall 66%effectiveness in preventing moderate to severe COVID-19 at 28 days after a single dose of AD26.COV2-S vaccine. The response rate for moderate-to-severe COVID-19 infection was 72% in the United States, 66% in Latin America, and reduced to 57% in South Africa(95% of mutant B.1.351). Two randomized placebo-controlled trials conducted by Novavax and Johnson in South Africa reported interim efficacy showing[19] that nvX-COV2373 vaccine was 49% effective in preventing mild, moderate, and severe COVID-19 infection with the B.1.351 variant, increasing to 60% when HIV-positive subjects were excluded.

3.3 Gamma (P.1) variant

Lineages P.1, a derivative of the B.1.1.28 variant, were first reported in Japanese travellers returning from the Brazilian Amazon. B.1.1.28 variant had 10 mutations in S protein (L18F, T20N, P26S, D138Y,R190S, H655Y, T1027I V1176, K417T, E484K and N501Y).Among them, three mutations (K417T, E484K and N501Y) located in the S protein RBD showed striking similarities with the B.1.351 variant RBD. Among them, the E484K mutation was proved to reduce the neutralization ability of antibodies to the virus. In samples collected at Manaus, the P.1 variant was reported to be 1.4-2.2 times more infectious, and was also found to evade 25-61% of acquired immunity. The neutralization effect of Moderna Moderna vaccine mRNA-1273 and Pfizer vaccine BNT162b2 on P.1 variant was significantly reduced[15] .

3.4 Delta (B.1.617.2) variant

The B.1.617.2 variant was first detected in India in October 2020 and caused the second wave of COVID-19 infection in India in April 2021, which then spread rapidly and attracted global attention.It was 97 percent more transmissible than the previous epidemic strain.Three key mutations (L452R, T478K and P681R) in the S protein of the B.1.617.2 variant reduced the probability of reinfection and the effectiveness of the vaccine.

The study shown[27],Vaccination with Pfizer vaccine BNT162b2 showed a low serum neutralization titer, but was still neutralized by the convalescent serum of most vaccinated individuals. Wall et al[28],Showed that after inoculated with two doses of Pfizer vaccine BNT162b2, the effective rate against B.1.617.2 vaiant was 87.9%,and the effective rate against B.1.1.7 lineage variant was 93.4%, but it did not prove that the reduction of neutralization would lead to the loss of vaccine efficacy against the disease. The effective rate of Johnson ＆ Johnson vaccine AD26.coV2-S against B.1.617.2 vaiant was 60%.The Oxford-Astrazeneca vaccine AZD1222 is 60-71%effective against the B.1.617.2 variant and can reduce severe cases.Sheikh et al[29],Showed that the B.1.617.2 variant was mainly present in younger and richer groups, and the risk of hospitalization of patients infected with B.1.617.2 variant was approximately doubled compared with that of patients infected with B.1.1.7, especially those with other diseases. Although Oxford-Astrazeneca vaccine AZD1222 and Pfizer vaccine BNT162b2 were both effective in reducing the risk of infection and hospitalization with the B.1.617.2 variant, the level of protection provided by the vaccine was significantly lower than that provided by the B.1.1.7 variant.

3.5 Omicron (B.1.1.529) variant

On November 9, 2021, a novel Coronavirus B.1.1.529 variant was detected for the first time from case samples in South Africa. The vaiant has grown so rapidly that it became the dominant strain of COVID-19 cases in Gauteng province in South Africa in just two weeks, and is now spreading around the world, making it the most severe mutation to date[30]. It is 500 percent more infectious than the original strain. The genome of the vaiant has about 50 mutations,including more than 30 mutations in the S protein, which overlap with the B.1.617.2 and B.1.1.7 variants[31].Previous studies have shown[25] that mutations in Novel coronavirusS protein K417N,E484K, or N501Y suggest enhanced immune escape. The triple mutation of K417N + E484AK+ N501Y was found in B.1.1.529.In addition, there are several other mutations that may reduce the neutralization activity of some monoclonal antibodies, the superposition of mutations may reduce the protective efficacy of some antibody drugs against the B.1.1.529 variant, and many site mutations in S protein may weaken the efficacy of existing vaccines[32].Studies have shown[33] that After inoculated with Moderna vaccine mRNA-1273, Pfizer vaccine BNT162b2 or Johnson ＆Johnson vaccine AD26.cov2.s primary vaccine series, The B.1.1.529 variant completely evades vaccine-induced immunity and appears to be more infectious in vitro, thus increasing the likelihood of increased transmissible activity. It should be noted that breakthrough infection with the B.1.1.529 variant may reduce the severity of disease in vaccinators due to cellular and innate immunity, despite the absence of humoral immunity.However, neutralizing antibodies remain the main relevance in preventing infection. In addition,a third dose of mRNA-based vaccine effectively produced a potent cross-neutralization response against the B.1.1.529 variant, possibly by increasing the breadth and cross-reactivity of the neutralizing antibody. Studies have also shown[34] that the neutralization activity of two doses of BNT162b2 and Moderna vaccine against B. 1.1.529 was reduced by 30 times. In the second dose of the new champions league vaccine after six months, serum from unvaccinated subjects did not show on B. 1.1.529 variants and activity, and restore the vaccinated individuals and activity decreased by 22 times, more than half of the subjects kept neutralizing antibody response, after the third agent to strengthen the new crown vaccine, The neutralizing activity of the B.1.1.529 variant was 14 times reduced, and more than 90% of subjects showed increased neutralizing activity against the B.1.1.529 variant. Thus, a third dose of COVID-19 vaccine provides a powerful neutralizing antibody response against the B.1.1.529 variant. Some studies have pointed out that although the B.1.1.529 variant has many mutations, it is still not a new subtype, which has not reached the point of immune escape and vaccine failure, and the existing COVID-19 vaccines still have some protective effect at present[35].

4. Summary and Prospect

COVID-19 is an emerging infectious disease caused by severe acute respiratory syndrome coronavirus 2. Serious threat to human life and health and social and economic development. As the COVID-19 pandemic continues, SARS-CoV-2 continues to evolve and mutate during transmission, forming variants with increased infectivity, virulence and resistance to vaccines and neutralizing antibodies.Compared with the original strain, the rapid evolution and high frequency mutation of S protein of these mutant strains may change the amino acid sequence of neutralizing antibody epitope,and then reduce its sensitivity to neutralizing antibody, further affect the effectiveness of neutralizing antibody and vaccine, and make the epidemic prevention and economic burden more difficult. A number of studies have shown that the approved vaccine still provides immune protection against the mutant strain, but there is also a degree of immune evasion. In addition, a third dose of COVID-19 vaccine can produce a powerful neutralizing antibody response,which can effectively prevent severe cases. However, as the Novel Coronavirus continues to mutate, which can cause the vaccine to lose its effectiveness, timely monitoring and analysis of the mutated strains will enable us to optimize our vaccine development strategy and provide a powerful weapon to defeat the outbreak.