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Sanger Sequencing for Molecular Diagnosis of SARS-CoV-2 Omicron Subvariants and Its Challenges
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作者 Sin Hang Lee 《Journal of Biosciences and Medicines》 CAS 2022年第9期182-223,共42页
Large population passages of the SARS-CoV-2 in the past two and a half years have allowed the circulating virus to accumulate an increasing number of mutations in its genome. The most recently emerging Omicron subvari... Large population passages of the SARS-CoV-2 in the past two and a half years have allowed the circulating virus to accumulate an increasing number of mutations in its genome. The most recently emerging Omicron subvariants have the highest number of mutations in the Spike (S) protein gene and these mutations mainly occur in the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the S gene. The European Centre for Disease Prevention and Control (eCDC) and the World Health Organization (WHO) recommend partial Sanger sequencing of the SARS-CoV-2 S gene RBD and NTD on the polymerase chain reaction (PCR)-positive samples in diagnostic laboratories as a practical means of determining the variants of concern to monitor possible increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them. The author’s diagnostic laboratory has implemented the eCDC/WHO recommendation by sequencing a 398-base segment of the N gene for the definitive detection of SARS-CoV-2 in clinical samples, and sequencing a 445-base segment of the RBD and a 490 - 509-base segment of the NTD for variant determination. This paper presents 5 selective cases to illustrate the challenges of using Sanger sequencing to diagnose Omicron subvariants when the samples harbor a high level of co-existing minor subvariant sequences with multi-allelic single nucleotide polymorphisms (SNPs) or possible recombinant Omicron subvariants containing a BA.2 RBD and an atypical BA.1 NTD, which can only be detected by using specially designed PCR primers. In addition, Sanger sequencing may reveal unclassified subvariants, such as BA.4/BA.5 with L84I mutation in the S gene NTD. The current large-scale surveillance programs using next-generation sequencing (NGS) do not face similar problems because NGS focuses on deriving consensus sequence. 展开更多
关键词 eCDC WHO Sanger Sequencing Omicron Variant Minor subvariants BA.4/BA.5 L84I BA.2 Multi-Allelic RECOMBINANT
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A spike-trimer protein-based tetravalent COVID-19 vaccine elicits enhanced breadth of neutralization against SARS-CoV-2 Omicron subvariants and other variants 被引量:6
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作者 Rui Wang Hongpeng Huang +13 位作者 Chulin Yu Chunyun Sun Juan Ma Desheng Kong Yalong Lin Dandan Zhao Shaozheng Zhou Jianbo Lu Sai Cao Yanjing Zhang Chunxia Luo Xuefeng Li Yang Wang Liangzhi Xie 《Science China(Life Sciences)》 SCIE CAS CSCD 2023年第8期1818-1830,共13页
Multivalent vaccines combining crucial mutations from phylogenetically divergent variants could be an effective approach to defend against existing and future SARS-Co V-2 variants.In this study,we developed a tetraval... Multivalent vaccines combining crucial mutations from phylogenetically divergent variants could be an effective approach to defend against existing and future SARS-Co V-2 variants.In this study,we developed a tetravalent COVID-19 vaccine SCTV01E,based on the trimeric Spike protein of SARS-Co V-2 variants Alpha,Beta,Delta,and Omicron BA.1,with a squalenebased oil-in-water adjuvant SCT-VA02B.In the immunogenicity studies in na?ve BALB/c and C57BL/6J mice,SCTV01E exhibited the most favorable immunogenic characteristics to induce balanced and broad-spectrum neutralizing potencies against pre-Omicron variants(D614G,Alpha,Beta,and Delta)and newly emerging Omicron subvariants(BA.1,BA.1.1,BA.2,BA.3,and BA.4/5).Booster studies in C57BL/6J mice previously immunized with D614G monovalent vaccine demonstrated superior neutralizing capacities of SCTV01E against Omicron subvariants,compared with the D614G booster regimen.Furthermore,SCTV01E vaccination elicited na?ve and central memory T cell responses to SARS-Co V-2 ancestral strain and Omicron spike peptides.Together,our comprehensive immunogenicity evaluation results indicate that SCTV01E could become an important COVID-19 vaccine platform to combat surging infections caused by the highly immune evasive BA.4/5 variants.SCTV01E is currently being studied in a head-to-head immunogenicity comparison phase 3 clinical study with inactivated and m RNA vaccines(NCT05323461). 展开更多
关键词 tetravalent SARS-CoV-2 vaccine Omicron subvariants broad neutralization
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Global challenge with the SARS-CoV-2 omicron BA.2(B.1.1.529.2)subvariant:Should we be concerned?
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作者 Jalil Roohani Masoud Keikha 《World Journal of Virology》 2022年第6期496-501,共6页
BA.2 is a novel omicron offshoot of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)that has gone viral.There is limited knowledge regarding this variant of concern.Current evidence suggests that this varia... BA.2 is a novel omicron offshoot of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)that has gone viral.There is limited knowledge regarding this variant of concern.Current evidence suggests that this variant is more contagious but less severe than previous SARS-CoV-2 variants.However,there is concern regarding the virus mutations that could influence pathogenicity,transmissibility,and immune evasion. 展开更多
关键词 SARS-CoV-2 Omicron BA.2 B.1.1.529.2 Subvariant
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Boosting with Omicron-specific mRNA vaccine or historical SARS-CoV-2 vaccines elicits discriminating immune responses against Omicron variants
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作者 Yi Wu Xiaoying Jia +10 位作者 Namei Wu Xinghai Zhang Yan Wu Yang Liu Minmin Zhou Yanqiong Shen Entao Li Wei Wang Jiaming Lan Yucai Wang Sandra Chiu 《Acta Pharmaceutica Sinica B》 2025年第2期947-962,共16页
Booster vaccinations are highly recommended in combating the SARS-CoV-2 Omicron variant and its subvariants.However,the optimal booster vaccination strategies and related immune mechanisms with different prior vaccina... Booster vaccinations are highly recommended in combating the SARS-CoV-2 Omicron variant and its subvariants.However,the optimal booster vaccination strategies and related immune mechanisms with different prior vaccinations are under-revealed.In this study,we systematically evaluated the immune responses in mice and hamsters with different prime-boost regimens before their protective efficacies against Omicron were detected.We found that boosting with Ad5-nCoV,S_(WT)-2P or SOmicron-6P induced significantly higher levels of neutralization activities against Omicron variants than CoronaVac and ZF2001 by eliciting stronger germinal center(GC)responses.Specifically,S_(Omicron)-6P induced even stronger antibody responses against Omicron variants in CoronaVac and Ad5-nCoV-primed animals than non-Omicron-specific vaccines but with limited differences as compared to Ad5-nCoV and SWT-2P.In addition,boosting with a specific vaccine has the potential to remodel the existing immune profiles.These findings indicated that adenovirus-vectored vaccines and mRNA vaccines would be more effective than other types of vaccines as booster shots in combating Omicron infections.Moreover,the protective efficacies of the vaccines in booster vaccinations are highly related to GC reactions in secondary lymphatic organs.In summary,these findings provide timely important information on prime-boost regimens and future vaccine design. 展开更多
关键词 SARS-CoV-2 Omicron subvariants Omicron-specific mRNA vaccine Commercial vaccines Booster vaccination Immune response
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Neutralizing antibody responses to three XBB protein vaccines in older adults
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作者 Guo-Jian Yang Mei Lu +8 位作者 Rui-Rui Chen Shuang-Qing Wang Sheng Wan Xue-Dong Song Guo-Ping Cao Lei Lv Xue-Juan He Bing-Dong Zhan Mai-Juan Ma 《Signal Transduction and Targeted Therapy》 2025年第3期1541-1551,共11页
The ongoing COVID-19 pandemic has underscored the importance of strong immune defenses against emerging SARS-CoV-2 variants.While COVID-19 vaccines containing XBB subvariants have proven effective in neutralizing new ... The ongoing COVID-19 pandemic has underscored the importance of strong immune defenses against emerging SARS-CoV-2 variants.While COVID-19 vaccines containing XBB subvariants have proven effective in neutralizing new SARS-CoV-2 variants,a gap remains in knowledge regarding neutralizing antibody responses in older adults aged>65 years against these newly emerged variants.This study was therefore undertaken to investigate and compare neutralizing antibody responses to three XBB-containing protein-based vaccines(trivalent XBB.1.5 vaccine,bivalent Omicron XBB vaccine,and tetravalent XBB.1 vaccine)head-to-head in 90 individuals aged>65 years.The results showed that all three XBB-containing vaccines substantially enhanced the neutralizing antibody response,with 100%of vaccinees having detectable antibody titers against ancestral D614G and variants BA.5,XBB.1.5,JN.1,KP.2,and KP.3 after booster immunization.Subsequent analysis indicated that the trivalent XBB.1.5 and tetravalent XBB.1 vaccines elicited higher levels of neutralizing antibodies compared to the bivalent Omicron XBB vaccine.The KP.2 and KP.3 variants displayed antibody resistance comparable to the JN.1 variant.Older adults produce similar neutralizing antibody responses to the vaccines regardless of their underlying medical conditions.These findings indicate that booster vaccination with XBB-containing vaccines can effectively elicit strong neutralizing responses against a number of SARS-CoV-2 variants in older adults over 65 years,which will help guide vaccine strategies in this elderly population. 展开更多
关键词 strong immune defenses neutralizing antibody responses immune defense xbb subvariants xbb protein vaccines older adults COVID emerging SARS CoV variants
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Original Antigenic Sin on Antibody Response in SARS-CoV-2 Infection
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作者 Miao Wang Huimin Guo +1 位作者 Bin Ju Zheng Zhang 《Infectious Diseases & Immunity》 CSCD 2024年第3期132-137,共6页
Infection and vaccination can provide protective immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of SARS-CoV-2 variants has persisted, leading to breakthrough infe... Infection and vaccination can provide protective immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the emergence of SARS-CoV-2 variants has persisted, leading to breakthrough infections. Owing to the original antigenic sin (OAS), variant breakthrough infection or vaccination potentially induces a stronger antibody response against the ancestral strain than to subsequent variants, as in the case of influenza. Thus, overcoming OAS is important for the development of future vaccine designs. This review summarizes the recent findings on OAS in the antibody response to SARS-CoV-2 and its variants, with an emphasis on future vaccine designs. 展开更多
关键词 SARS-CoV-2 Original antigenic sin Antibody response Omicron subvariants Vaccine design
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Quantification and Differentiation of SARS-CoV‑2 Variants in Wastewater for Surveillance 被引量:1
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作者 Teresa Kumblathan Yanming Liu +3 位作者 Xiaoli Pang Steve E.Hrudey XChris Le Xing-Fang Li 《Environment & Health》 2023年第3期203-213,共11页
Wastewater surveillance plays an important role in the monitoring of infections of SARS-CoV-2 at the community level.We report here the determination of SARS-CoV-2 and differentiation of its variants of concern in 294... Wastewater surveillance plays an important role in the monitoring of infections of SARS-CoV-2 at the community level.We report here the determination of SARS-CoV-2 and differentiation of its variants of concern in 294 wastewater samples collected from two major Canadian cities from May 2021 to March 2023.The overall method of analysis involved extraction of the virus and viral components using electronegative membranes,in situ stabilization and concentration of the viral RNA onto magnetic beads,and direct analysis of the viral RNA on the magnetic beads.Multiplex reverse transcription quantitative polymerase chain reaction(RT-qPCR)assays,targeting specific and naturally selected mutations in SARS-CoV-2,enabled detection and differentiation of the Alpha,Beta,Gamma,Delta,and Omicron variants.An Omicron triplex RT-qPCR assay targeting three mutations,HV 69−70 deletion,K417N,and L452R,was able to detect and differentiate the Omicron BA.1/BA.3,BA.2/XBB,and BA.4/5.This assay had efficiencies of 90−104%for all three mutation targets and a limit of detection of 28 RNA copies per reaction.Analyses of 294 wastewater samples collected over a two-year span showed the concentrations and trends of Alpha,Beta,Gamma,Delta,and Omicron variants as they emerge in two major Canadian cities participating in the wastewater surveillance program.The trends of specific variants were consistent with clinical reports for the same period.At the beginning of each wave,the corresponding variants were detectable in wastewater.For example,RNA concentrations of the BA.2 variant were as high as 10^(4)copies per 100 mL of wastewater collected in January 2022,when approximately only 50−60 clinical cases of BA.2 infection were reported in Canada.These results show that the strategy and highly sensitive assays for the variants of concern in wastewater are potentially useful for the detection of newly emerging SARS-CoV-2 variants and other viruses for future community biomonitoring. 展开更多
关键词 COVID-19 SARS-CoV-2 variants of concern Omicron subvariants multiplex RT-qPCR wastewater surveillance
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Dynamic Humoral Immune Response to Primary and Booster Inactivated SARS-CoV-2 Vaccination in Patients with Cirrhosis
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作者 Qian Zhu Lu Wang +10 位作者 Xiaoxiao Hu Yingzhi Zhang Tianquan Huang Taiyu He Zhiwei Chen Gaoli Zhang Mingli Peng Min Chen Dachuan Cai Xiaofeng Shi Hong Ren 《Journal of Clinical and Translational Hepatology》 SCIE 2023年第7期1476-1484,共9页
Background and Aims:Our aim was to determine the immune efficacy of a severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)booster vaccination in cirrhotic patients who had received the primary series.Methods:We... Background and Aims:Our aim was to determine the immune efficacy of a severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)booster vaccination in cirrhotic patients who had received the primary series.Methods:We performed a longitudinal assessment in 48 patients with cirrhosis,57 patients with chronic hepatitis B(CHB)and 68 healthy controls(HCs)to continuously track the dynamics of SARS-CoV-2 specific antibodies and memory B cells after receiving the primary series and booster dose at different times.A pseudovirus neutralization assay was used to determine neutralization against Omicron subvariants BA.2.12.1,BA.4 and BA.5 from serum samples collected from three cohorts.Results:Serum anti-receptor-binding domain(RBD)immunoglobulin(Ig)G and neutralizing antibody(NAb)levels in cirrhotic patients were elevated within 15–45 days after completing the primary series before rapidly declining and reaching a valley at around 165–195 days.After receiving the booster dose,both antibody levels were significantly increased to levels comparable to patients with CHB and HCs.Subgroup analysis showed that booster vaccination induced weaker antibody responses in patients with decompensated cirrhosis than in those with compensated cirrhosis.The SARS-CoV-2 memory B-cell response in cirrhotic patients was durable during follow-up regardless of the hepatic fibrocirrhosis grade.However,compared with the primary series,the booster dose did not result in an evident improvement of neutralization activity against the Omicron subvariants BA.2.12.1 and BA.4,and was followed by a significant decrease in the titer against BA.5.Conclusions:A booster dose elicited a robust and durable humoral response to the wild-type strain in cirrhotic patients but not the Omicron subvariants.Repeated vaccination of inactivated SARS-CoV-2 vaccine may not benefit cirrhotic patients in neutralization against newly circulating strains. 展开更多
关键词 SARS-CoV-2 Omicron subvariants CIRRHOSIS Booster dose Humoral response
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An imported human case with the SARS-CoV-2 Omicron subvariant BA.2.75 in Yunnan Province,China
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作者 Meiling Zhang Zhixiao Chen +8 位作者 Jienan Zhou Xiaonan Zhao Yaoyao Chen Yanhong Sun Zhaosheng Liu Wenpeng Gu Chunrui Luo Xiaoqing Fu Xiang Zhao 《Biosafety and Health》 CSCD 2022年第6期406-409,共4页
The Omicron variants spread rapidly worldwide after being initially detected in South Africa in November 2021.It showed increased transmissibility and immune evasion with far more amino acid mutations in the spike(S)p... The Omicron variants spread rapidly worldwide after being initially detected in South Africa in November 2021.It showed increased transmissibility and immune evasion with far more amino acid mutations in the spike(S)protein than the previously circulating variants of concern(VOCs).Notably,on 15 July 2022,we monitored the first VOC/Omicron subvariant BA.2.75 in China from an imported case.Moreover,nowadays,this subvariant still is predominant in India.It has nine additional mutations in the S protein compared to BA.2,three of which(W152R,G446S,and R493Q reversion)might contribute to higher transmissibility and immune escape.This subvariant could cause wider spread and pose a threat to the global situation.Our timely reporting and continuous genomic analysis are essential to fully elucidate the characteristics of the subvariant BA.2.75 in the future. 展开更多
关键词 SARS-CoV-2 Omicron subvariant MUTATIONS Genomic analysis
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