Virological Characteristics and Prevention and Control of Omicron Sub-lineage BA.2

Xiao-Wen Yao, Rong Wang, Cai-Hong Wang, Yu-Xia Zhou, Xiao-Hui Yu, Jiu-Cong Zhang✉

Keywords:Omicron BA.2 Characteristics Vaccine effectiveness Monoclonal antibodies

ABSTRACT The Omicron sub-lineage BA.2 has caused a new round of infection of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2), leading to a surge in the number of COVID-19 cases in many countries, including China. Because the subvariant BA.2 shows strong infectivity, fast transmission, strong immune escape ability, relatively mild symptoms, strong concealment,difficult to find and so on, it has gradually become a new challenge during the COVID-19 pandemic. Understanding the virological characteristics of Omicron sub-lineage BA.2 is of great significance for epidemic prevention and control. This paper briefly summarizes the virological characteristics and prevention and control strategies of Omicron sub-lineage BA.2.✉Corresponding author: ZHANG Jiu-cong, M.D., Postdoctoral Fellow, Deputy Chief Physician, Associate Professor, Postgraduate Tutor.

The pandemic of COVID-19 (Coronavirus disease 2019) poses a great threat to global public health. As of March 15, 2022, the cumulative number of confirmed cases worldwide has reached 470 million[1]. COVID-19 was caused by severe acute respiratory syndrome coronavirus 2. With the continuous evolution of SARSCoV-2, a number of highly infectious and pathogenic mutants appeared. Among them, the mutants with stronger transmissibility and pathogenicity are classified as "concerned variants" (Variant of Concern,VOC) by the World Health Organization (World health organization,WHO), including Alpha (B.1.1.7), Beta (B.1.351),Gamma (P.1), Delta (B.1.617.2 ), Lambda (C.37) and Omicron(B.1.1.529) mutant[2]. The Omicron mutant was first discovered in Africa in early November 2021 and quickly became the main pathogenic strain of COVID-19 in the world. WHO designated the Omicron mutant as the fifth "VOC" on November 26th, 2021. At present, there are many subvariants of Omicron, including BA.1(B.1.1.529.1), BA.1.1 (B.1.1.529.1.1), BA.2 (B.1.1.529.2) and BA.3(B.1.1.529.3)[3]. The number of people infected with subvariant BA.2 showed a rising trend in many countries and regions. It brings great challenges to the prevention and control of the epidemic. This paper briefly describes the virological characteristics of Omicron subvariant BA.2.

1. Main sublines and characteristic mutations of Omicron mutants

At present, the Omicron mutant has become a major concern mutant in the world, including several subvariants with significantly different genetic characteristics: BA.1, BA.1.1, BA.2 and BA.3. As of March 26, 2022, the cumulative prevalence of BA.1 accounted for 12% (detected in at least 158countries), BA.1.1 accounted for 10% (detected in at least 145countries), BA.2 accounted for 5%(detected in at least 103countries), and BA.3 accounted for less than 0.5% (detected in at least 21 countries) [4]. According to the latest data of GISAID, the characteristic mutations of the main subvariants of Omicron mutants were analyzed, and it was found that the subvariants BA.2 and BA.1 had significant diversity.BA.3 has no specific mutation and is a combination of spike protein mutations in BA.1 and BA.2 lineages. There were 30, 29 and 19 mutations on Omicron subvariants BA.1, BA.2 and BA.3,respectively. BA.1.1 shares 30 mutations from BA.1, and there is a unique mutation: R346K. Omicron subvariants BA.1 and BA.2 contain 19 mutations (G142D, G339D, S373P, S375F, S477N,T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y,N679K, P681H, N764K, D796Y, Q954H and N969K) in the receptor binding domain (Receptor-binding domain,RBD) of spike protein. Among them, N501Y and Q498R mutations have been shown to enhance the binding to the Angiotensin converting enzyme 2 receptor of angiotensin converting enzyme 2, while N679K and P681H mutations of H655Y can increase spike cleavage and promote virus transmission[5]. BA.1 has five mutation sites (S371L,G496S, T547K, N856K and L981F) different from BA.2 and BA.3,which may be the key to the initial transmission of BA.1 which is significantly higher than that of the other two subvariants.

The Omicron subvariant BA.2 has 10 unique RBD mutation sites:T19I, L24S, del25/27, V213G, S371F, T376A, D405N, K417N,N440K and R408S. RBD is the main target of therapeutic antibodies and antibodies induced by vaccination or infection. These unique mutations are the key to affect the therapeutic monoclonal antibody and vaccine effectiveness of the Omicron subvariant BA.2. However,there is no del69/70 in the subvariant BA.2 spike protein, but both BA.1 and BA.3. This makes BA.1 and BA.3 subvariants appear spike protein gene off-target (S gene target failure,SGTF) in nucleic acid polymerase chain reaction (Polymerase chain reaction,PCR)detection, which is an important feature different from other variants such as Delta, so it is easy to be found. However, the subvariant BA.2 genome does not have SGTF, which makes it more difficult to identify BA.2 in PCR detection[6]. Therefore, the Omicron subvariant BA.2, also known as the "invisible mutant", requires more complex and time-consuming methods such as gene sequencing to be identified[7].

2. Characteristics of subvariant BA.2

BA.2, a subvariant of Omicron, caused a new round of infection of SARS-CoV-2, which led to a surge in the number of COVID-19 cases in many countries, and gradually dominated all parts of the world, including parts of Europe. Because the subvariant BA.2 has the characteristics of strong infectivity, fast transmission,strong immune escape ability, and relatively mild symptoms, strong concealment, difficult to find and so on, it has gradually become a new challenge during the COVID-19 pandemic.

2.1 Epidemiology

With the relaxation of the prevention and control of the epidemic situation of COVID-19, the Omicron subvariant BA.2 spread rapidly as soon as it appeared, resulting in a sharp increase in the number of patients infected with COVID-19 in some European countries,including Italy, France, the Netherlands and Switzerland. In one week from March 14 to March 20, 2022, the number of COVID-19 cases in Italy increased by 43 per cent compared with the beginning of this month, while the number of COVID-19 cases in France increased by 36 per cent[8]. At the same time, according to the monitoring data of the Global Influenza data sharing Initiative, the UK has reported 137726 cases of subvariant BA.2 novel coronavirus variant infection, which is currently the country with the largest number of cases of subvariant BA.2 infection in the world[9]. As early as March 6, 2022, more than 80 per cent of new confirmed cases of subvariant BA.2 were reported each week in the UK[10].According to data released by the US Centers for Disease Control and Prevention (CDC) on March 22nd, more than 1/3 of the new confirmed cases of COVID-19 in the United States were infected with Omicron subvariant BA.2. The subvariant BA.2 of Omicron in New England and New York in the northeastern United States accounted for more than half of all new infections[11].

Omicron subvariant BA.2 is replacing the original subvariant BA.1 to dominate all over the world, including the United Kingdom,Denmark, Germany, Sweden and China[8]. Denmark is the first country where subvariant BA.2 infection has replaced BA.1.Since the first case of infection with subvariant BA.2 was found in Denmark on December 5, 2021, the prevalence of BA.2 in less than 10 weeks has increased from less than 0.1% to 89.2%in sequenced samples[12]. In mid-January 2022, the first case of Omicron subvariant BA.2 was found in Hong Kong, China. Despite the immediate adoption of stringent public health measures, the spread of BA.2 was not controlled and even led the fifth wave of outbreaks in Hong Kong[13]. The Omicron subvariant BA.2 spread rapidly in Hong Kong with a doubling time of 3.4 days, and the number of new cases per day increased exponentially. According to data from the Centre for Health Protection of the Hong Kong Department of Health, the number of COVID-19 infections reported in the fifth wave of the epidemic in Hong Kong from December 31, 2021 to zero on March 15, 2022 has exceeded 748000, with more than 27000 new cases on March 14. During the 49 days from March 1 to April 18, 2022, a total of more than 497000 indigenous infections were reported nationwide, affecting 31 provinces. Among them, the epidemic situation in Shang Hai is still at a high level,and the risk of community transmission is still high. More than 27000 local confirmed cases and more than 370000 asymptomatic infections have been reported[14]. For several consecutive days, the number of new infections in Shanghai has exceeded 2000 every day, and the number of asymptomatic infections has increased by more than 20, 000 a day. The situation of prevention and control is still grim. The epidemic situation in Ji Lin Province showed an overall downward trend, and the epidemic situation in He Bei, Jiang Su, Zhe Jiang and An Hui provinces tended to be stable, but the impact of cross-input between regions was obvious, and the risk of community transmission persisted in the places where the epidemic occurred[15]. At present, the epidemic situation of COVID-19 caused by subvariant BA.2 is rising rapidly, and the situation of prevention and control at home and abroad is still very grim.

2.2 Infection

Omicron subvariant BA.2 is one of the most contagious varieties at present. Jilin Provincial Centers for Disease Control and Prevention reported that the subvariant BA.2 is 30% more contagious than BA.1 and has stronger transmission. If community transmission occurs, the number of cases of infection can double within 2 to 3 days[16]. At the same time, Chen[17] et al found that the infectivity of subvariant BA.2 was 4.2 and 1.5 times higher than that of Delta mutant and subvariant BA.1, respectively. Zhang Wenhong said that the basic transmission number (R0 value) of BA.2, a subvariant of the epidemic in Shanghai, was 9.5, which was 3 to 5 times that of the original strain. In addition, the binding free energy (BFE)between RBD and ACE2 is proportional to the infectivity of the virus[18]. By detecting the BFE changes of RBD-ACE2 complex caused by Omicron mutant, other major mutants of SARS-CoV-2 and RBD mutation of Omicron subvariant, it was found that the BFE value of subvariant BA.2 was much higher than that of other mutants of SRAS-CoV-2, and it was one of the most infectious variants at present[17].

Patients infected with Omicron subvariant BA.2 are more likely to be infected with family contacts. A survey by the British Health and Safety Agency found that the infection rate of family contacts with the subvariant BA.2 was 13.4% (within 2 to 7 days of exposure),which was higher than that of the subvariant BA.1 (10.3%)[19]. In addition, Lyngse[20]investigated the epidemic situation of family aggregation in Denmark from the end of December 2021 to early January 2022 and found that the secondary attack rate (SAR) of family contacts in families infected with Omicron subvariant BA.2 was about 39%, which was higher than that of family contacts infected with subvariant BA.1 (29%). In addition, a Danish study found that the subvariant BA.2 can also reinfect cured patients who had previously been infected with BA.1, and most of those who were reinfected with BA.2 after BA.1 infection were under 20 years old and unvaccinated[21]. Therefore, we expect that the subvariant BA.2 of Omicron may eventually replace the subvariant BA.1 of Omicron and become the next dominant variant of COVID-19 pandemic in the world.

2.3 Pathogenicity

The Weekly Epidemiological report of COVID-19 published by WHO on March 8, 2022 showed that the disease severity of Omicron mutants was lower than that of Delta mutants[22]. The Department of Health and Safety said there was no evidence of an increase in hospitalization rates among UK patients infected with the subvariant BA.1 compared with the subvariant BA.2[23]. At the same time, the Danish National Serum Institute studied 932 patients with COVID-19 and found that there was no difference in hospitalization risk between subvariants BA.1 and BA.2[24]. Jiao Yahui, director of the Medical Administration of the National Health Commission,said that as of the morning of March 15, 2022, more than 95% of the 8201 hospitalized cases in Jilin Province were asymptomatic infections and mild cases[25]. According to the Daily Mail on March 10th, the case fatality rate of COVID-19 in the UK has dropped sevenfold to 0.03%, which is lower than that of influenza. However,the average age of admission of patients infected with subvariant BA.2 was significantly lower than that of patients infected with BA.1(40 years old to 51 years old).

Compared with the original strain of early SARS-CoV-2, the subvariant BA.2 of Omicron has lower pathogenicity, which may be related to the difference of mutation sites. Spike protein mediates the attachment and membrane fusion of virus and ACE2 receptor,which enables the virus to enter the host cell and is the main target of antibodies caused by host immune response. The mutation of spike protein can affect the transmission and pathogenicity of the virus[26].It was found that among the common mutations of the subvariant BA.2 spike protein, Q493R, N501Y, Q498R, T478K and Y505H had the highest binding affinity to ACE2 receptors, which may increase infectivity and transmission. E484K mutation can lead to partial immune escape by reducing the binding of neutralizing antibodies,which is beneficial to reinfection[27]. However, the binding affinity of N440K and E484 mutations to ACE2 receptor was the lowest[28].However, the interaction between different mutations seems to restore the ACE2 binding efficiency lost due to other changes such as K417N and Y505H. In addition, K417N, E484A and Q493R are very destructive to many antibodies[17]. Among the unique mutations of the subvariant BA.2 spike protein, the affinity of the S477N mutation to the host cell decreased, the affinity of the D405N mutation to the ACE2 receptor was the lowest, and the T376A, D405N and R408S mutations may reduce the potency of many antibodies[17]. T76I mutation affects the efficiency of antibody binding and contributes to immune escape. It has been confirmed that the ability of Omicron subvariant BA.2 to evade the current vaccine is also 30% higher than that of Omicron subvariant BA.1 and 17 times higher than that of Delta mutant. In addition, the viral load test showed that compared with the initial infection, the concentration of Omicron subvariant BA.2 reinfection was lower than that of BA.1 infection[20].

2.4 Effectiveness of the vaccine

Vaccination is an important and effective tool to prevent and limit SARS-CoV-2 infection. COVID-19 vaccines are generally highly effective, especially in the prevention of serious illness,hospitalization and death. A survey of Danish families found that individuals who were fully vaccinated and vaccinated with booster had a higher susceptibility to BA.2, BA.1. Compared with the vaccinated individuals, the unvaccinated individuals were more susceptible to the subvariant BA.2. Data provided by the UK Health and Safety Agency found that the protection rate of the two doses of the vaccine against subvariant BA.2 was limited, and the effective rate of the vaccine against subvariant BA.2 was reduced to 13%after 25 weeks of vaccination, while the effectiveness of the vaccine against subvariant BA.2 infection increased to 70% two weeks after the third dose of enhanced injection[18].

The Omicron subvariant BA.2 also has the characteristic of immune escape, which further reduces the protective effect of vaccination on infection. The study found that the subvariant BA.2 could increase the escape ability of the current vaccine by 27 times, and the escape ability of the current vaccine was about 30% higher than that of BA.1 and 17 times higher than that of Delta[19]. Yamasoba and other experiments showed that the subvariant BA.2 was highly resistant to the antiserum induced by mRNA-1273 and ChAdOx1 vaccine, and the neutralizing antibody ability of BA.2 was 18 times and 24 times lower than that of the original strain, respectively[29]. Yu[30] found that the neutralizing antibody titer of subvariant BA.2 decreased 27 times after two doses of Pfizer vaccine, and the neutralizing antibody titer of BA.2 decreased to less than 20 six months after inoculation,while the neutralizing antibody titer of subvariant BA.2 decreased 8.4 times two weeks after three doses of Pfizer vaccine, which was 1.4 times lower than that of BA.1. At the same time, the neutralizing antibody titer in the serum of individuals infected with subvariant BA.1 was 1.3 times lower than that of BA.2 on the 4th day after infection. It can be seen that individuals infected with subvariant BA.1 produce cross-immunity to BA.2, that is, to provide strong protection against subvariant BA.2 reinfection, and the defense effect will be better after vaccination.

2.5 Monoclonal antibody drugs and antiviral drugs

The development and application of antiviral drugs and monoclonal antibody drugs bring hope to contain the pandemic of COVID-19. However, with the emergence of more contagious mutants, the mutations in the spike protein sites of these mutants make it easier for the mutants to escape the protective immune response. Omicron mutants have mutations in RNA-dependent RNA polymerase (RdRp)and SARS-CoV-2 major proteases, which are targeted by antiviral drugs[31]. However, the subvariant BA.2 has many more specific mutations than the Omicron mutant, which raises concerns about the effectiveness of existing antiviral drugs against the subvariant BA.2 of Omicron. At present, the antiviral drugs Molnupiravir and Nirmatrelvir are authorized by the US Food and Drug Administration(FDA) for emergency treatment of COVID-19[32]. In the hamster model infected with SARS-CoV-2, monopivir and nemativir not only greatly reduced the viral load in hamster lungs, but also effectively inhibited the viral replication of hamster lower respiratory tract subvariant BA.2. In addition, 3CL protease inhibitor Smai 217622 is a candidate drug for oral anti-novel coronavirus, which obtains the emergency use right of FDA. Smur217622 had antiviral activity against a variety of mutants. It was found that the hamster infected with subvariant BA.2 decreased upper respiratory tract infection and even the virus titer in turbinate decreased significantly after treatment with Smur217622[33].

The research and development of monoclonal antibodies is an important part of anti-SARS-CoV-2. However, monoclonal antibodies are prone to viral mutations, especially those with antibody resistance. The subvariant BA.2 was almost completely resistant to Cassirizumab and Ivid Monoclonal (Imdevimab)[28]. It was reported that the neutralizing activity of three broad-spectrum neutralizing McAbs (Sotrovimab, S2X259 and S2H97) against Omicron mutants remained unchanged, while the effectiveness of other McAbs against Omicron mutants decreased[34]. In February 2022, FDA authorized the emergency use of four neutralizing antibody drugs against novel coronavirus: Sotrovimab,Bebtelovimab, REGEN-COV (Casirivimab/Imdevimab) and Evusheld (Tixagevimab/Cilgavimab)[28]. It was found that the resistance of the subvariant BA.2 to Sotrovimab was 35 times higher than that of the original strain[25]. FDA shows that Sotrovimab therapy is not effective in hospitalized patients with subvariant BA.2 infection, and the clinical outcome is poor when it is used in hospitalized patients with COVID-19 who need high flow oxygen or mechanical ventilation. Therefore, on April 5, 2022, FDA will no longer authorize Sotrovimab to be used in the United States for COVID-19 treatment[35]. The 50% focus reduction neutralization test (FRNT50) refers to the relative dilution of the serum needed to neutralize 50% virus. The higher the FRNT50 titer, the more effective the serum against a specific virus. Patients with subvariant BA.2 infection had a serum FRNT50titer 43 to 143.6 times higher than that of the original SARS-CoV-2 strain and other VOC after treatment with REGEN-COV antibody cocktail therapy. It can be seen that REGEN-COV antibody cocktail therapy can effectively inhibit Omicron subvariant BA.2. Evusheld had a lower FRNT50value for the subvariant BA.2, which was 1.4 to 8.1 times higher than that of the original strain and VOC[36]. The neutralization activity of therapeutic monoclonal antibodies (REGEN-COV and Evusheld)to subvariant BA.2 was lower than that to early mutant strains,which could effectively inhibit virus infection in respiratory organs of golden hamsters infected with subvariant BA.2[33]. It has been found that this therapeutic monoclonal antibody is effective against OmicronBA.2 mutants.

3. Prevention and control strategies to deal with subvariant BA.2

The subvariant BA.2 of Omicron has the characteristics of highly contagious, strong immune escape ability, strong concealment,difficult to find and so on, resulting in a sharp increase in the number of COVID-19 cases at home and abroad. Because of its mild pathogenicity, many patients do not show clinical symptoms in the early stage, but they are still contagious and more concealed, which has caused more infections when they were found. The presence of asymptomatic patients greatly increases the risk of the epidemic.Therefore, we should take more measures to deal with the prevention and control of the subvariant BA.2, mainly adopting the general strategy of "external defense input, internal defense rebound" and the general policy of "dynamic zero clearance". To prevent further spread of the epidemic: first, to achieve regular prevention and control of the epidemic in key places, key units and key groups, with special emphasis on isolation and observation of entry personnel and strengthening daily surveillance of people involved in the transportation of cold chains or goods outside the country. strengthen health surveillance, vaccination, nucleic acid testing, cleaning and disinfection and emergency disposal to curb local transmission caused by overseas imports. Second, publicize and educate COVID-19 on prevention and control knowledge through various channels,improve people's awareness of self-epidemic prevention and health literacy, advocate people to wear masks, wash hands frequently,provide more ventilation, "one meter line", avoid large-scale gathering activities, etc.; third, people without contraindications are encouraged to be vaccinated and vaccinated to strengthen needles,especially those in key units in key places, so as to reduce the risk of infection and disease. Fourth, do a good job in self-protection,and if you find symptoms such as redness and swelling of the throat or pain and cough, you can use the antigen screening method to do self-examination. if you find positive, you should report it to the local epidemic prevention department in time for timely disposal;fifth, strengthen scientific research, do a good job in the iteration of testing reagents, and increase the sensitivity of detection to avoid missed detection. Sixth, strengthen the research and development of effective vaccines and drugs to deal with Omicron variants and their different subvariants and even future unknown variants.

4. Summary

The emergence and spread of Omicron subvariant BA.2 has led to a surge in the number of COVID-19 cases in many countries and regions, which has brought great challenges to the global epidemic prevention and control and threatened human health. Because of its strong infectivity, fast transmission speed, low pathogenicity and strong concealment, it increases the difficulty of epidemic prevention and control. Therefore, timely and effective epidemic prevention and control measures are particularly important to curb the infection and spread of Omicron subvariant BA.2. According to the current severe and complex epidemic situation in the world, vaccination is still one of the important means for our epidemic prevention and control.