The SARS-CoV-2 Omicron variants are notorious for their transmissibility,but little is known about their subgenomic RNA(sgRNA)expression.This study applied RNA-seq to delineate the quantitative and qualitative profile...The SARS-CoV-2 Omicron variants are notorious for their transmissibility,but little is known about their subgenomic RNA(sgRNA)expression.This study applied RNA-seq to delineate the quantitative and qualitative profiles of canonical sgRNA of 118 respiratory samples collected from patients infected with Omicron BA.2 and compared with 338 patients infected with non-variant of concern(non-VOC)-D614G.A unique characteristic profile depicted by the relative abundance of 9 canonical sgRNAs was reproduced by both BA.2 and non-VOCD614G regardless of host gender,age and presence of pneumonia.Remarkably,such profile was lost in samples with low viral load,suggesting a potential application of sgRNA pattern to indicate viral activity of individual patient at a specific time point.A characteristic qualitative profile of canonical sgRNAs was also reproduced by both BA.2 and non-VOC-D614G.The presence of a full set of canonical sgRNAs carried a coherent correlation with crude viral load(AUC¼0.91,95%CI 0.88–0.94),and sgRNA ORF7b was identified to be the best surrogate marker allowing feasible routine application in characterizing the infection status of individual patient.Further potentials in using sgRNA as a target for vaccine and antiviral development are worth pursuing.展开更多
The SARS-CoV-2 virus,particularly the Omicron BA.2 variant,led to a significant surge in Shanghai,2022.However,the viral load dynamic in Omicron infections with varying clinical severities remain unclear.This prospect...The SARS-CoV-2 virus,particularly the Omicron BA.2 variant,led to a significant surge in Shanghai,2022.However,the viral load dynamic in Omicron infections with varying clinical severities remain unclear.This prospective cohort included 48,830 hospitalized coronavirus disease 2019(COVID-19)patients across three hospitals in Shanghai,China,between 23 March and 15 May,2022.Systematic nucleic acid testing was performed using RT-PCR Cycle threshold(Ct)value as a proxy of viral load.We analyzed the kinetic characteristics of viral shedding by clinical severity and identified associated risk factors.The study comprised 31.06%asymptomatic cases,67.66%mild-moderate cases,1.00%severe cases,0.29%critical and fatal cases.Upon admission,57%of patients tested positive,with peak viral load observed at 4 days(median Ct value 27.5),followed by a decrease and an average viral shedding time(VST)of 6.1 days(Interquartile range,4.0–8.8 days).Although viral load exhibited variation by age and clinical severity,peak Ct values occurred at similar times.Unvaccinated status,age exceeding 60,and comorbidities including hypertension,renal issues kidney dialysis and kidney transplantation,neurological disorders,rheumatism,and psychotic conditions were found to correlate with elevated peak viral load and extended VST.Asymptomatic cases demonstrated a 40%likelihood of contagiousness within 6 days of detection,while mild-moderate and severe cases exhibited post-symptom resolution infectious probabilities of 27%and over 50%,respectively.These findings revealed that the initial Ct values serve as a predictive indicator of severe outcomes.Unvaccinated elderly individuals with particular comorbidities are at high-risk for elevated viral load and prolonged VST.展开更多
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
目的本研究旨在评估基于新冠病毒原始毒株与奥密克戎(Omicron)变异株开发的SARS-CoV-2抗体检测试剂,在未接种疫苗的艾滋病病毒感染者(people living with HIV,PLWH)感染Omicron变异株后的检测性能。方法本研究招募了45名未接种新冠疫苗...目的本研究旨在评估基于新冠病毒原始毒株与奥密克戎(Omicron)变异株开发的SARS-CoV-2抗体检测试剂,在未接种疫苗的艾滋病病毒感染者(people living with HIV,PLWH)感染Omicron变异株后的检测性能。方法本研究招募了45名未接种新冠疫苗、首次感染Omicron BA.5毒株的PLWH,并在4个月后进行随访。使用八种针对原始毒株和两种针对Omicron毒株的抗体试剂检测抗体水平,并以针对原始毒株(wild-type,WT)、BA.4/5和XBB.1.5的假病毒中和实验为金标准,使用McNemar与Kappa检验定性结果的一致性,使用斯皮尔曼(Spearman)相关性分析定量结果的相关性。结果原始毒株抗体试剂与WT中和抗体(neutralizing antibody,nAb)的一致性最高(κ值最高为0.483),与Omicron-nAb的一致性明显较低。在定量分析中,原始毒株抗体试剂与WT-nAb呈强相关(r_(s)=0.69~0.85),而与BA.4/5(r_(s)=0.40~0.57)和XBB.1.5(r_(s)=0.43~0.63)-nAb的相关性较弱。二次感染后,原始毒株抗体试剂与Omicron-nAb之间的相关性有所提升。Omicron特异性抗体试剂与Omicron-nAb的95%一致性界限更窄。结论在未接种疫苗的PLWH中,原始毒株抗体试剂对Omicron感染后的免疫应答检测存在局限性,研究结果支持开发和应用变异株特异性抗体试剂,以实现更准确的免疫监测和评估。展开更多
Background:SARS-CoV-2,first identified in late 2019,has given rise to numerous variants of concern(VOCs),posing a significant threat to human health.The emer-gence of Omicron BA.1.1 towards the end of 2021 led to a pa...Background:SARS-CoV-2,first identified in late 2019,has given rise to numerous variants of concern(VOCs),posing a significant threat to human health.The emer-gence of Omicron BA.1.1 towards the end of 2021 led to a pandemic in early 2022.At present,the lethal mouse model for the study of SARS-CoV-2 needs supplementation,and the alterations in neutrophils and monocytes caused by different strains remain to be elucidated.Methods:Human ACE2 transgenic mice were inoculated with the SARS-CoV-2 proto-type and Omicron BA.1,respectively.The pathogenicity of the two strains was evalu-ated by observing clinical symptoms,viral load and pathology.Complete blood count,immunohistochemistry and flow cytometry were performed to detect the alterations of neutrophils and monocytes caused by the two strains.Results:Our findings revealed that Omicron BA.1 exhibited significantly lower vir-ulence compared to the SARS-CoV-2 prototype in the mouse model.Additionally,we observed a significant increase in the proportion of neutrophils late in infection with the SARS-CoV-2 prototype and Omicron BA.1.We found that the proportion of monocytes increased at first and then decreased.The trends in the changes in the proportions of neutrophils and monocytes induced by the two strains were similar.Conclusion:Our study provides valuable insights into the utility of mouse models for simulating the severe disease of SARS-CoV-2 prototype infection and the milder manifestation associated with Omicron BA.1.SARS-CoV-2 prototype and Omicron BA.1 resulted in similar trends in the changes in neutrophils and monocytes.展开更多
SARS-CoV-2 remains prevalent,with highly diverse strains carrying spike proteins with antigenic profiles distinct from those of the original strain(Wuhan Hu-1 or WT).Since November 2021,Omicron has acquired a remarkab...SARS-CoV-2 remains prevalent,with highly diverse strains carrying spike proteins with antigenic profiles distinct from those of the original strain(Wuhan Hu-1 or WT).Since November 2021,Omicron has acquired a remarkable capacity to outcompete previous SARS-CoV-2 and has become the dominant variant globally[1].Extensive studies have provided insights into how the adult immune system,particularly humoral immunity,respond to SARS-CoV-2 and its variants,including Omicron[2].展开更多
Objective To investigate whether Omicron BA.1 breakthrough infection after receiving the SARS-CoV-2 vaccine could create a strong immunity barrier.Methods Blood samples were collected at two different time points from...Objective To investigate whether Omicron BA.1 breakthrough infection after receiving the SARS-CoV-2 vaccine could create a strong immunity barrier.Methods Blood samples were collected at two different time points from 124 Omicron BA.1 breakthrough infected patients and 124 controls matched for age,gender,and vaccination profile.Live virus-neutralizing antibodies against five SARS-CoV-2 variants,including WT,Gamma,Beta,Delta,and Omicron BA.1,and T-lymphocyte lymphocyte counts in both groups were measured and statistically analyzed.Results The neutralizing antibody titers against five different variants of SARS-CoV-2 were significantly increased in the vaccinated population infected with the Omicron BA.1 variant at 3 months after infection,but mainly increased the antibody level against the WT strain,and the antibody against the Omicron strain was the lowest.The neutralizing antibody level decreased rapidly 6 months after infection.The T-lymphocyte cell counts of patients with mild and moderate disease recovered at 3 months and completely returned to the normal state at 6 months.Conclusion Omicron BA.1 breakthrough infection mainly evoked humoral immune memory in the original strain after vaccination and hardly produced neutralizing antibodies specific to Omicron BA.1.Neutralizing antibodies against the different strains declined rapidly and showed features similar to those of influenza.Thus,T-lymphocytes may play an important role in recovery.展开更多
目的建立重组Omicron BA.4/5-Delta株新冠疫苗体外相对效力的检测方法,并进行验证,以期为替代体内效力检测奠定基础。方法以人源单克隆抗体GH4作为包被抗体,HRP标记的CB6人源单克隆抗体作为酶标抗体的双抗体夹心ELISA法为基础,确定疫苗...目的建立重组Omicron BA.4/5-Delta株新冠疫苗体外相对效力的检测方法,并进行验证,以期为替代体内效力检测奠定基础。方法以人源单克隆抗体GH4作为包被抗体,HRP标记的CB6人源单克隆抗体作为酶标抗体的双抗体夹心ELISA法为基础,确定疫苗解吸附方法;再以该解吸附方法结合双抗体夹心ELISA法建立体外相对效力检测方法。并验证方法的线性范围、专属性、准确性、精密性、耐用性及定量限。采用建立的方法检测3批供试品重组Omicron BA.4/5-Delta株新冠疫苗的体外相对效力。结果确定解吸附方法为:将疫苗与处理液(1.25 mL 20%二乙醇胺,0.20 mL 10%Triton X-100,8.55 mL PBS)按等体积分数混合,于25℃解离30 min,解吸附率可达95%以上。疫苗参考品在1~26 ng/mL浓度范围内,与A_(450)呈良好的线性关系,线性方程为log(y)=1.447 log(x)-1.643,R^(2)为0.998;可特异性检测疫苗参考品的体外相对效力;90000、50000和20000 ng/mL浓度疫苗参比品检测结果的回收率均在80%~120%范围内;重复性及中间精密性验证相对标准偏差(relative standard deviation,RSD)均<20%;解离条件、检测体系孵育时间和显色时间发生微小变动时,检测结果不受影响;定量限为0.2。批号为J202301002、J202301003、J202301004供试品的体外相对效力分别为1.0,1.0和0.8,RSD为11%。结论建立的用于检测体外相对效力的方法具有良好的准确性、精密性、专属性和耐用性,可用于重组Omicron BA.4/5-Delta株新冠疫苗体外相对效力的检测。展开更多
基金supported by the Food and Health Bureau,Hong Kong SAR Government(reference no.COVID19F06).
文摘The SARS-CoV-2 Omicron variants are notorious for their transmissibility,but little is known about their subgenomic RNA(sgRNA)expression.This study applied RNA-seq to delineate the quantitative and qualitative profiles of canonical sgRNA of 118 respiratory samples collected from patients infected with Omicron BA.2 and compared with 338 patients infected with non-variant of concern(non-VOC)-D614G.A unique characteristic profile depicted by the relative abundance of 9 canonical sgRNAs was reproduced by both BA.2 and non-VOCD614G regardless of host gender,age and presence of pneumonia.Remarkably,such profile was lost in samples with low viral load,suggesting a potential application of sgRNA pattern to indicate viral activity of individual patient at a specific time point.A characteristic qualitative profile of canonical sgRNAs was also reproduced by both BA.2 and non-VOC-D614G.The presence of a full set of canonical sgRNAs carried a coherent correlation with crude viral load(AUC¼0.91,95%CI 0.88–0.94),and sgRNA ORF7b was identified to be the best surrogate marker allowing feasible routine application in characterizing the infection status of individual patient.Further potentials in using sgRNA as a target for vaccine and antiviral development are worth pursuing.
基金financial support from the Key Program of the National Natural Science Foundation of China(82130093)Wenhong Zhang,Juanjuan Zhang acknowledge financial support from Shanghai Municipal Science and Technology Major Project(HS2021SHZX001)+2 种基金Wenhong Zhang acknowledges financial support from the Key Program of the National Natural Science Foundation of China(82161138018 and 82041010)Shanghai Science and Technology Committee(20dz2260100,20Z11901100)Shanghai Hospital Development Center(SHDC2020 CR5010-002).
文摘The SARS-CoV-2 virus,particularly the Omicron BA.2 variant,led to a significant surge in Shanghai,2022.However,the viral load dynamic in Omicron infections with varying clinical severities remain unclear.This prospective cohort included 48,830 hospitalized coronavirus disease 2019(COVID-19)patients across three hospitals in Shanghai,China,between 23 March and 15 May,2022.Systematic nucleic acid testing was performed using RT-PCR Cycle threshold(Ct)value as a proxy of viral load.We analyzed the kinetic characteristics of viral shedding by clinical severity and identified associated risk factors.The study comprised 31.06%asymptomatic cases,67.66%mild-moderate cases,1.00%severe cases,0.29%critical and fatal cases.Upon admission,57%of patients tested positive,with peak viral load observed at 4 days(median Ct value 27.5),followed by a decrease and an average viral shedding time(VST)of 6.1 days(Interquartile range,4.0–8.8 days).Although viral load exhibited variation by age and clinical severity,peak Ct values occurred at similar times.Unvaccinated status,age exceeding 60,and comorbidities including hypertension,renal issues kidney dialysis and kidney transplantation,neurological disorders,rheumatism,and psychotic conditions were found to correlate with elevated peak viral load and extended VST.Asymptomatic cases demonstrated a 40%likelihood of contagiousness within 6 days of detection,while mild-moderate and severe cases exhibited post-symptom resolution infectious probabilities of 27%and over 50%,respectively.These findings revealed that the initial Ct values serve as a predictive indicator of severe outcomes.Unvaccinated elderly individuals with particular comorbidities are at high-risk for elevated viral load and prolonged VST.
文摘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.
文摘目的本研究旨在评估基于新冠病毒原始毒株与奥密克戎(Omicron)变异株开发的SARS-CoV-2抗体检测试剂,在未接种疫苗的艾滋病病毒感染者(people living with HIV,PLWH)感染Omicron变异株后的检测性能。方法本研究招募了45名未接种新冠疫苗、首次感染Omicron BA.5毒株的PLWH,并在4个月后进行随访。使用八种针对原始毒株和两种针对Omicron毒株的抗体试剂检测抗体水平,并以针对原始毒株(wild-type,WT)、BA.4/5和XBB.1.5的假病毒中和实验为金标准,使用McNemar与Kappa检验定性结果的一致性,使用斯皮尔曼(Spearman)相关性分析定量结果的相关性。结果原始毒株抗体试剂与WT中和抗体(neutralizing antibody,nAb)的一致性最高(κ值最高为0.483),与Omicron-nAb的一致性明显较低。在定量分析中,原始毒株抗体试剂与WT-nAb呈强相关(r_(s)=0.69~0.85),而与BA.4/5(r_(s)=0.40~0.57)和XBB.1.5(r_(s)=0.43~0.63)-nAb的相关性较弱。二次感染后,原始毒株抗体试剂与Omicron-nAb之间的相关性有所提升。Omicron特异性抗体试剂与Omicron-nAb的95%一致性界限更窄。结论在未接种疫苗的PLWH中,原始毒株抗体试剂对Omicron感染后的免疫应答检测存在局限性,研究结果支持开发和应用变异株特异性抗体试剂,以实现更准确的免疫监测和评估。
基金supported by Beijing Natural Science Foundation(Grant No.Z210014)National Natural Science Foundation of China(Grant No.32070543)+1 种基金National Key Research and Development Project of China(Grant No.2022YFC2303404)CAMS Innovation Fund for Medical Sciences(CIFMS)(Grant No.2022-12M-CoV19-002)
文摘Background:SARS-CoV-2,first identified in late 2019,has given rise to numerous variants of concern(VOCs),posing a significant threat to human health.The emer-gence of Omicron BA.1.1 towards the end of 2021 led to a pandemic in early 2022.At present,the lethal mouse model for the study of SARS-CoV-2 needs supplementation,and the alterations in neutrophils and monocytes caused by different strains remain to be elucidated.Methods:Human ACE2 transgenic mice were inoculated with the SARS-CoV-2 proto-type and Omicron BA.1,respectively.The pathogenicity of the two strains was evalu-ated by observing clinical symptoms,viral load and pathology.Complete blood count,immunohistochemistry and flow cytometry were performed to detect the alterations of neutrophils and monocytes caused by the two strains.Results:Our findings revealed that Omicron BA.1 exhibited significantly lower vir-ulence compared to the SARS-CoV-2 prototype in the mouse model.Additionally,we observed a significant increase in the proportion of neutrophils late in infection with the SARS-CoV-2 prototype and Omicron BA.1.We found that the proportion of monocytes increased at first and then decreased.The trends in the changes in the proportions of neutrophils and monocytes induced by the two strains were similar.Conclusion:Our study provides valuable insights into the utility of mouse models for simulating the severe disease of SARS-CoV-2 prototype infection and the milder manifestation associated with Omicron BA.1.SARS-CoV-2 prototype and Omicron BA.1 resulted in similar trends in the changes in neutrophils and monocytes.
基金supported by the National Key Research and Development Program of China(Grant Nos.2021YFC2701800 and 2022YFC2703603)the National Natural Science Foundation of China(Grant Nos.32270991,32100751 and 32100123)the Shanghai Science and Technology Innovation Action(Grant Nos.21JC1405800 and 21ZR1470600).
文摘SARS-CoV-2 remains prevalent,with highly diverse strains carrying spike proteins with antigenic profiles distinct from those of the original strain(Wuhan Hu-1 or WT).Since November 2021,Omicron has acquired a remarkable capacity to outcompete previous SARS-CoV-2 and has become the dominant variant globally[1].Extensive studies have provided insights into how the adult immune system,particularly humoral immunity,respond to SARS-CoV-2 and its variants,including Omicron[2].
基金funded by the Emergency prevention and cure Program of COVID-19[22ZXGBSY00010]Tianjin Medical Key Discipline Project[TJYXZDXK-50A]sponsored by Tianjin Municipal Science and Technology Bureau and Tianjin Municipal Health Commission,respectively.
文摘Objective To investigate whether Omicron BA.1 breakthrough infection after receiving the SARS-CoV-2 vaccine could create a strong immunity barrier.Methods Blood samples were collected at two different time points from 124 Omicron BA.1 breakthrough infected patients and 124 controls matched for age,gender,and vaccination profile.Live virus-neutralizing antibodies against five SARS-CoV-2 variants,including WT,Gamma,Beta,Delta,and Omicron BA.1,and T-lymphocyte lymphocyte counts in both groups were measured and statistically analyzed.Results The neutralizing antibody titers against five different variants of SARS-CoV-2 were significantly increased in the vaccinated population infected with the Omicron BA.1 variant at 3 months after infection,but mainly increased the antibody level against the WT strain,and the antibody against the Omicron strain was the lowest.The neutralizing antibody level decreased rapidly 6 months after infection.The T-lymphocyte cell counts of patients with mild and moderate disease recovered at 3 months and completely returned to the normal state at 6 months.Conclusion Omicron BA.1 breakthrough infection mainly evoked humoral immune memory in the original strain after vaccination and hardly produced neutralizing antibodies specific to Omicron BA.1.Neutralizing antibodies against the different strains declined rapidly and showed features similar to those of influenza.Thus,T-lymphocytes may play an important role in recovery.
文摘目的建立重组Omicron BA.4/5-Delta株新冠疫苗体外相对效力的检测方法,并进行验证,以期为替代体内效力检测奠定基础。方法以人源单克隆抗体GH4作为包被抗体,HRP标记的CB6人源单克隆抗体作为酶标抗体的双抗体夹心ELISA法为基础,确定疫苗解吸附方法;再以该解吸附方法结合双抗体夹心ELISA法建立体外相对效力检测方法。并验证方法的线性范围、专属性、准确性、精密性、耐用性及定量限。采用建立的方法检测3批供试品重组Omicron BA.4/5-Delta株新冠疫苗的体外相对效力。结果确定解吸附方法为:将疫苗与处理液(1.25 mL 20%二乙醇胺,0.20 mL 10%Triton X-100,8.55 mL PBS)按等体积分数混合,于25℃解离30 min,解吸附率可达95%以上。疫苗参考品在1~26 ng/mL浓度范围内,与A_(450)呈良好的线性关系,线性方程为log(y)=1.447 log(x)-1.643,R^(2)为0.998;可特异性检测疫苗参考品的体外相对效力;90000、50000和20000 ng/mL浓度疫苗参比品检测结果的回收率均在80%~120%范围内;重复性及中间精密性验证相对标准偏差(relative standard deviation,RSD)均<20%;解离条件、检测体系孵育时间和显色时间发生微小变动时,检测结果不受影响;定量限为0.2。批号为J202301002、J202301003、J202301004供试品的体外相对效力分别为1.0,1.0和0.8,RSD为11%。结论建立的用于检测体外相对效力的方法具有良好的准确性、精密性、专属性和耐用性,可用于重组Omicron BA.4/5-Delta株新冠疫苗体外相对效力的检测。
