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
Since the outbreak of COVID-19,with the emergence of a series of novel coronavirus variants of different types,COVID-19 has continued to spread across the globe,posing a huge threat to the lives and health of people a...Since the outbreak of COVID-19,with the emergence of a series of novel coronavirus variants of different types,COVID-19 has continued to spread across the globe,posing a huge threat to the lives and health of people around the world and posing a severe challenge to global public health security.Recently,the World Health Organization(WHO)announced that novel coronavirus variant strain"Omicron"subtype variant strain BA.2 has been found in 57 countries and regions.It has higher vaccine and antibody tolerance and is more infectious than omicron(B.1.1.529).In this paper,we briefly review the recent studies on the omicron subtype variant strain BA.2.展开更多
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.Beca...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.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
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.
基金The 940th Hospital Intra-Hospital Fund Project(No.20yjky020)the Huoshenshan Hospital Research Fund General Project(No.HSS-217)。
文摘Since the outbreak of COVID-19,with the emergence of a series of novel coronavirus variants of different types,COVID-19 has continued to spread across the globe,posing a huge threat to the lives and health of people around the world and posing a severe challenge to global public health security.Recently,the World Health Organization(WHO)announced that novel coronavirus variant strain"Omicron"subtype variant strain BA.2 has been found in 57 countries and regions.It has higher vaccine and antibody tolerance and is more infectious than omicron(B.1.1.529).In this paper,we briefly review the recent studies on the omicron subtype variant strain BA.2.
基金General Project of Huoshenshan Hospital Scientific Research Fund(No.HSS-217)New Crown Fund Project of No.940 Hospital(No.20yjky020)。
文摘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.
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.
