Recent research progress on subtypes of Omicron

Jun Huang, Xue-Feng Ma, Hui-Juan Shao, Na Li, Xiao-Hui Yu, Jiu-Cong Zhang✉

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

Keywords:COVID-19 Omicron Variant Subtype Progress

A BSTRACT

At the end of 2019, Coronavirus Disease 2019(COVID-19) caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has become a major global public health event. As of March 29,2022, the number of confirmed cases in the world has exceeded 480 million, and the total number of deaths has exceeded 6.12 million[1]. Novel coronavirus has undergone evolution and variation in the process of transmission, and has formed many variant strains.In November 9, 2021, South Africa firstly detected a variant strain(B.1.1.529) from a sample of cases. In November 26, the World Health Organization named it "Omicron variant strain", It is defined as the fifth "variant of concern (VOC)" after Alpha, Beta, Gamma and Delta. This variant strain has a large number of mutations and leads to harmful changes in epidemiology. At present, this variant strain has spread in 128 countries and has become the main epidemic variant strain in the world. Omicron variant strain consists of several subtypes, including BA.1, BA.2 and BA.3 [2]. Since January 2022, BA.1 has replaced Delta as the main transmission variant strain in the world, and recently, The proportion of BA.2 relative to BA.1 has been increasing, as of February 14, 2022, BA.2 has become the main epidemic variant strain in dozens of countries and regions, including Denmark, India, Philippines, Brunei and other countries. Omicron variant strain is highly transmissible and can escape the defense of the immune system, the effectiveness of vaccine against Omicron variant strain is lower [3]. The subtypes of Omicron variant strain have different mutation and infectivity.Therefore, it is very important for public health, epidemic prevention and control to understand the subtypes of Omicron variant strain and its immune escape mechanism as soon as possible. This article reviews the characteristics and immune escape mechanisms of each Omicron variant strain subtype.

1. Structure and etiology of SARS-CoV-2

Sars-cov-2 is a kind of positive-sense single-stranded RNA virus,belong to β Coronavirus, and it is a coronavirus with envelope and spherical particles with a diameter of 100-160nm. The genome length of Sars-cov-2 is about 30000 nucleotides, There are two non-translated regions (5 '-UTR and 3' -UTR) and six open reading frames (ORFs). The first ORF1a/b is at the 5 'end and is responsible for encoding nonstructural proteins. The other ORFs encode accessory proteins and four essential structural proteins, including spike protein (S), envelope protein (E), membrane protein (M) and nucleocapsid protein (N). M protein is involved in the formation of virus envelope, E protein is responsible for the production and release of virus particles, and N protein is involved in the replication cycle of virus [4, 5]. S protein includes two subunits of S1 and S2. S1 contains N-terminal domain (NTD) and receptor-binding domain(RBD), which are responsible for recognizing host cell receptors,RBD can bind the ACE2 receptor on the host cell membrane,resulting in the conformational change of S2, thus promoting the fusion of virus and host cell membrane, then the RNA of virus enter the host cell [6]. S protein is the determinant of virus transmission and immune escape, the variation of its structure can change the infectivity of the virus and occur immune escape [7]. At present,S protein and its RBD region are still the main targets for the development of vaccines and monoclonal antibodies [8].

2. Subtypes of Omicron variant strain

Omicron variant strain were mainly divided into three subtypes,B.1.1.529.1, B.1.1.529.2 and B.1.1.529.3, named BA.1,BA. 2 and BA.3. They branch out from the same B.1.1 node and evolve along independent branches [9].

2.1 Characteristics of BA.1

BA.1 was first detected in South Africa on November 9, 2021.In the following week, nearly 300 cases of Omicron were found in more than 30 countries and regions outside South Africa. This variant strain was quickly listed as VOC by the World Health Organization, and became the main transmission variant strain in the world instead of Delta in January 2021. Currently BA.1 has spread in more than 100 countries and remains the most common subtype reported worldwide [10].

The replication speed of BA.1 in human bronchial tissue is about 70 times faster compared with Delta variant strain and original strain, the transmission of BA.1 is higher. The Israeli Ministry of health released a news that the infectivity of Omicron is about 30%higher than Delta [11]. Hu et al.[12] compared the replication ability of BA.1 and previous variant strains in vitro explant cultures of human bronchus and lung, found BA.1 has faster and higher virus replication efficiency in human bronchus, which indicates that it has the ability to enhance transmission. Compared with Delta, the low replication ability of BA.1 in human lungs may be the main reason for asymptomatic or mild symptoms in patients infected with Omicron. Migueres et al.[13] compared the virological characteristics of Omicron and Delta, found that Omicron was more infectious,not because the virus shed more in the nasopharynx, but mainly caused by S protein mutation. The mutation of Omicron RBD can enhance the affinity with ACE2 receptor, produce strong electrostatic interaction (salt bridge) and hydrogen bond, and form a stable complex, which provides a new basis for the high propagation force of Omicron [14].

Compared with the original Wuhan strain, BA.1 carries at least 60 mutations in the coding area and noncoding area, and there are at least 37 mutations in its S protein (including 30 amino acid substitutions, 3 deletions and 1 insertion). It is worth noting that 15 of the 30 amino acid substitutions are located in the RBD region, of which 5 (G446S,Q493R,G496S,Q498R,Y505H) have been proved to enhance the binding force with ACE2 receptor and immune escape [15,16]. Desingu et al.[17] analysis S protein of three subtypes,found that there were 37 mutations in S protein of BA.1, of which 21 mutations(G142D,G339D,S373P,S375F,K417N,N440K,S477N,T4 78K,E484A,Q493R,Q498R,N501Y,Y505H,D614G,H655Y,N679K,P681H,N764K,D796Y,Q954H,N969K)were common mutations in the three subtypes, and found 16 characteristic mutations(ins214EP E,S371L,G496S,T547K,N856K,L981F,A67V,H69del,V70del,T95I,V143del,Y144del,Y145del,N211I,L212Idel,G446S)in BA.1. Other structural proteins of BA. 1 also have mutations, including T9I in E protein, D3G, Q19E and A63T in M protein, many deletions (E31-, R32 -, S33 -) and mutations (P13L, R203K, G204R) in N protein[18].

Studies have shown that the mutations of H655Y, N679K, P681H in S protein of BA.1 can increase the ability of virus to enter host cells and make the virus have higher transmissibility. Mutations of S317L (characteristic mutation of BA.1), N501Y, S373P, S375F,E484A, Q498R, T478K can enhance the interaction between virus and ACE2 receptor. In addition, R203K and G204R mutations in N protein are related to the increase of virus load [17, 19, 20]. BA. 1 is the first subtype of Omicron, which has a large number of mutations relative to the previous mutant, resulting in highly transmissible of BA.1, and BA.1 quickly becomes the main epidemic variant strain in the world.

2.2 Characteristics of BA.2

BA.2 was found in South Africa in November 17, 2021. Before mid December 2021, according to the genome data of novel coronavirus uploaded to GISAID platform by various countries, BA.1 has always been the main Omicron subtype, BA.2 is very rare. As of February 14, 2022, BA.2 has become a major epidemic variant strain in dozens of countries and regions, including Denmark, India,Philippines, Brunei, Nepal, Pakistan and Bangladesh [21]. At present,BA.2 has spread to 93 countries and regions around the world,BA.2 has exceeded BA.1 in 43 countries of them [22].In China,since March 2022, the first local case of this round of epidemic has been found in Yanbian Prefecture, Jilin Province, Qingdao City,Shandong Province and Putuo District, Shanghai on the same day.Subsequently, the total number of infected people has continued to rise in Shandong, Guangdong, Hebei, Yunnan, Shanghai and other places, and most of them are BA.2 subtype [23].

Compared with Delta, the transmission speed of BA.1 is 77%faster, while the propagation speed of BA.2 is 66% faster than BA.1 in China [24]. According to the epidemic data of Denmark, The transmission power of BA.2 is 30% higher than that of BA.1 [25].Chen et al. [26] constructed a deep learning model based on algebraic topology, the BFE change of RBD-ACE2 complex induced by RBD mutation of BA.1,BA.2,BA.3, the greater the BFE change, the higher the infectivity, it was found that the changes of BFE of BA.1, BA.2,BA.3 were 2.60, 2.98 and 2.88 kcal / mol, respectively BA.2 has the highest infectivity, is about 1.5 times that of BA.1. At present, the infection rate of BA.2 has exceeded BA.1, which may replace BA.1 as the next major epidemic variant strain.

There were 31 mutations in S protein of BA.2, including 21 common mutations and 10 characteristic mutations(T19I,L24S,P25del,P26del,A27S,V213G,T376A,R408S,S371F,D405N)[17].Compared with the original Wuhan strain, all these mutations include the substitution or deletion of 7 amino acids in NTD, 16 amino acid substitution in RBD and D614G mutation, Three amino acid substitutions close to the furin cleavage site and four amino acid substitutions in the S2 region[27].Compared with BA.1 and BA.3,there is a deletion of 69-70 in S protein, while BA.2 does not have this mutation, which makes BA.2 more difficult to be identified in RT-PCR detection. Therefore, it is called "invisible Omicron" [28].Desingu et al.[29] systematically analyzed the genetic diversity of BA.2 and found that the ORF3a protein of BA.2 transmitted in Denmark contained a specific mutation called H78Y, which was not common in other countries and was mainly detected in Denmark and Sweden. The role of H78Y mutation in virus activity has not been reported, but ORF3 protein can promote virus release. Therefore,they speculated that the high infectivity of Denmark BA.2 may be related to the H78Y mutation on ORF3a.BA. The high infectivity of BA.2 and the difficulty of its detection have brought great obstacles to epidemic prevention and control. More research is needed to clarify its mechanism, so as to further guide the development of epidemic prevention in various countries.

2.3 Characteristics of BA.3

BA.3 was found in South Africa on November 18, 2021. Globally,there are few reports on the infection of BA.3. From the discovery to March 9, 2022, only about 500 patients were infected. In Denmark,BA.3 was not found until January 19, 2022 [30].

There are 33 mutations in S protein of BA.3, but there are no characteristic mutations in BA.3, sharing 10 characteristic mutations from BA.1 (A67V,H69del,V70del,T95I,V143del,Y144del,Y145d el,N211I,L212del,G446S) and two characteristic mutations from BA.2(S371F,D405N)[17]. Among the 33 mutations of BA.3, 31 mutations are common to BA.1. Therefore, it is speculated that the reason why the BA.3 spreads at a very low rate and leads to fewer cases may be due to the lack of six mutations of BA.1 (ins214EPE,S371L, G496S, T547K, N856K, L981F)or the acquisition of two mutations from BA.2 (S371F, D405N).Due to the limitation of the number of samples, there are few studies on BA.3 subtype.

3. Immune escape mechanism of Omicron mutant

After virus infection or vaccination, B lymphocytes will produce neutralizing antibodies and bind to the virus surface antigen, so as to block the combination of pathogen and host cell receptor and prevent pathogenic microorganisms from invading host cells. Most new coronavirus vaccines and monoclonal antibodies are developed for the S protein of the virus. The variation of S protein can enhance the affinity between the virus and ACE2, so as to competitively inhibit the binding of neutralizing antibody and S protein, and make the virus immune escape. In addition, mutation may also change the epitope of neutralizing antibody [18,20]. Cao et al. [31] used highthroughput yeast map screening to determine the RBD escape mutation spectrum of 247 neutralizing antibodies. It was found that various single mutations of Omicron would damage neutralizing antibodies at different epitopes, among which K417N, G446S,E484A and Q493R mutations were involved in immune escape. In addition, Y505H mutation can reduce the contact between the virus and the host antibody and enhance the ability of the virus to escape from the host immune system.

The mutation of S protein of Omicron subtypes lead to different tolerance of each subtype to vaccine and monoclonal antibody. Yu et al. [32] obtained samples from individuals inoculated with mRNA BNT162b2 vaccine, used BA.1 and BA.2 pseudovirus infection samples and measured the neutralizing antibody titer. It was found that the neutralizing antibody titer of BA.2 decreased by 1.3-1.4 times compared with BA.1. Chen et al. [26] induced BFE changes of RBD-ACE2 complex with RBD mutations of various subtypes. It was found that the negative cumulative BFE changes of all subtypes were more than the positive changes, indicating their antibody resistance. In the same environment, BA.1, BA.2 and BA.3 may increase their vaccine breakthrough ability by about 21, 27 and 18 times. BA.2 showed significant resistance to most therapeutic monoclonal antibodies, including Sotrovimab, but Sotrovimab maintained considerable effectiveness against BA.1. Except for Bebtelovimab, no other therapeutic monoclonal antibody can fully cover all Omicron variant strain subtypes [33]. The immune escape of Omicron variant strain hinders the effectiveness of vaccination and monoclonal antibody treatment. At present, more vaccines and drugs are needed to solve this problem.

4. Summary and Prospect

Omicron variant strain has caused a pandemic in the world. At present, the number of infections in various places is still increasing,and the number of BA.2 infections is also gradually increasing.At present, we still have little understanding of Omicron and its subtypes. Its high infectivity and high immune escape ability have brought great difficulties to epidemic prevention. El-shabasy et al. [19] analyzed 528176 cases of Omicron and 573012 cases of Delta and found that the proportion of hospitalized patients with Omicron infection was reduced by 68% after three doses of vaccine compared with those who were not vaccinated. The Omicron did not completely escape the existing vaccine, the completion of the whole vaccination can still effectively reduce the risk of hospitalization,severe illness and death caused by the Omicron variant strain, and strengthening the vaccination of needles can also effectively reduce the risk of breakthrough infection caused by the Omicron variant strain [34]. Therefore, active vaccination is still the most effective preventive measure. In addition, it is also very important to continue to maintain an appropriate social distance and wear masks when going out. At present, studies on the immune escape mechanism,detection, specific vaccines and therapeutic antibodies of Omicron and its subtypes are being carried out in an orderly manner. Some scholars have also developed a multiplex RT-qPCR assay for Omicron subtypes, which can be used to detect and distinguish Omicron subtypes [35]. Positive progress has also been made in specific vaccines against Omicron variant strain at home and abroad.China has made rapid progress in the research and development of univalent and multivalent vaccines against Omicron variant strain[36]. We firmly believe that through the joint efforts of the people of all countries, mankind will eventually overcome novel coronavirus.

Conflict of interest

All authors have no conflict of interest.

Author's contribution Jun Huang completed the writing of the paper and the analysis of literature; Xue-Feng Ma and Hui-Juan Shao and Na Li participated in the analysis of literature; Xiao-Hui Yu and Jiu-Cong Zhang participated in the topic selection and design, guided and revised the paper. All authors read and agreed to the final text.