Coronavirus disease 2019(COVID-19)is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).The gold standard method for the diagnosis of SARS-CoV-2 depends on quantitative r...Coronavirus disease 2019(COVID-19)is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).The gold standard method for the diagnosis of SARS-CoV-2 depends on quantitative reverse transcription-polymerase chain reaction till now,which is time-consuming and requires expensive instrumentation,and the confirmation of variants relies on further sequencing techniques.Herein,we first proposed a robust technique-methodology of electrochemical CRISPR sensing with the advantages of rapid,highly sensitivity and specificity for the detection of SARS-CoV-2 variant.To enhance the sensing capability,gold electrodes are uniformly decorated with electro-deposited gold nanoparticles.Using DNA template identical to SARS-CoV-2 Delta spike gene sequence as model,our biosensor exhibits excellent analytical detection limit(50 fM)and high linearity(R2=0.987)over six orders of magnitude dynamic range from 100 fM to 10 nM without any nucleic-acid-amplification assays.The detection can be completed within 1 h with high stability and specificity which benefits from the CRISPR-Cas system.Furthermore,based on the wireless micro-electrochemical platform,the proposed biosensor reveals promising application ability in point-of-care testing.展开更多
On January 22,2021,a 34-year-old male,who served as a security guard at the isolation point in Shenzhen,tested positive for coronavirus disease 2019(COVID-19)during the every-three-day routine test.After the nasophary...On January 22,2021,a 34-year-old male,who served as a security guard at the isolation point in Shenzhen,tested positive for coronavirus disease 2019(COVID-19)during the every-three-day routine test.After the nasopharyngeal swab was further confirmed as positive for COVID-19 by Shenzhen CDC,the patient was transferred to the Third People’s Hospital of Shenzhen and was diagnosed as a COVID-19 asymptomatic infection.On January 25,2021,Shenzhen CDC identified the 20H/501.Y.V2(B.1.351)variant,which was a variant of COVID-19 virus first emerging in the South Africa.展开更多
On June 14,2021,a customs officer(Case A)went to the infirmary at Baoan International Airport in Shenzhen due to a runny nose and fever.He was admitted to the Central Hospital of Baoan immediately.This patient prelimi...On June 14,2021,a customs officer(Case A)went to the infirmary at Baoan International Airport in Shenzhen due to a runny nose and fever.He was admitted to the Central Hospital of Baoan immediately.This patient preliminarily tested positive for coronavirus disease 2019(COVID-19)infection,caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),using a quantitative realtime reverse transcription polymerase chain reaction(qRT-PCR)method in this hospital.Then,a mixed specimen of nasopharyngeal swab.展开更多
Screening for coronavirus disease 2019(COVID-19)virus,also known as SARS-CoV-2,infection every seven days was performed for high-risk populations who worked at the Yantian Port in Yantian District,Shenzhen City,Guangd...Screening for coronavirus disease 2019(COVID-19)virus,also known as SARS-CoV-2,infection every seven days was performed for high-risk populations who worked at the Yantian Port in Yantian District,Shenzhen City,Guangdong Province.On May 20,2021,an oropharyngeal swab from a 44-year-old male(Case A)tested preliminarily positive for COVID-19 by a quantitative real-time reverse transcription polymerase chain reaction(RT-qPCR)method in a third-party laboratory.展开更多
The coronavirus disease 2019(COVID-19)caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis,bringing enormous burden to our society.Most patien...The coronavirus disease 2019(COVID-19)caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis,bringing enormous burden to our society.Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms.展开更多
Introduction:Human noroviruses are the leading cause of acute viral gastroenteritis(AGE)worldwide in all age groups.GII.4 strains have been the predominant genotype circulating globally over the last 2 decades and sin...Introduction:Human noroviruses are the leading cause of acute viral gastroenteritis(AGE)worldwide in all age groups.GII.4 strains have been the predominant genotype circulating globally over the last 2 decades and since 2012.GII.4 Sydney viruses have emerged and caused the majority of AGE outbreaks worldwide.Methods:Data from norovirus outbreaks from the laboratory-based surveillance of norovirus outbreaks in China(CaliciNet China)between October 2016–December 2020 were analyzed.Results:During October 2016–December 2020,1,954 norovirus outbreaks were reported,and positive fecal samples from 1,352(69.19%)outbreaks were genotyped.GII.4 Sydney[P31]viruses accounted for 2.1%(October 2016–August 2017),5.5%(September 2017–August 2018),3.3%(September 2018–August 2018),26.6%(September 2019–August 2020),and and 1.1%(September 2020–December 2020)of GII outbreaks,respectively.Compared to reference strains of GII.4 Sydney[P31]from 2012 to 2013,7 amino acid mutations in epitopes[A(297,372 and 373),B(333),E(414),and H(309 and 310)]and 1 in human histo-blood group antigens binding site at site II 372 were found by analyzing 9 GII.4 Sydney[P31]complete genomic sequences.Conclusions:This report identified the genomic variation of GII.4 Sydney[P31]from CaliciNet China.Continued surveillance with prompt genotyping and genetic analysis is necessary to monitor the emergence of novel GII.4 variants.展开更多
Dear Editor,The Omicron(B.1.1.529)variant of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)was first identified in November 2021,in South Africa and Botswana.The first Omicron sub-lineage that emerged was...Dear Editor,The Omicron(B.1.1.529)variant of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)was first identified in November 2021,in South Africa and Botswana.The first Omicron sub-lineage that emerged was BA.1,which was supplanted by BA.2 in many countries.One of the most notable features of the Omicron variant is its ability to evade neutralizing antibodies(nAbs)targeting the original virus lineages.展开更多
Introduction:Since 2019,numerous variants of concern for severe acute respiratory syndrome virus 2(SARS-CoV-2)have emerged,leading to significant outbreaks.The development of novel,highly accurate,and rapid detection ...Introduction:Since 2019,numerous variants of concern for severe acute respiratory syndrome virus 2(SARS-CoV-2)have emerged,leading to significant outbreaks.The development of novel,highly accurate,and rapid detection techniques for these new SARSCoV-2 variants remains a primary focus in the ongoing efforts to control and prevent the coronavirus disease 2019(COVID-19)pandemic.Methods:Reverse transcription-recombinase polymerase amplification combined with the clustered regularly interspaced short palindromic repeatsassociated protein 12a(CRISPR/Cas12a)system was used to validate the detection of the Omicron BA.2,BA.4,and BA.5 variants of SARS-CoV-2.Results:Our results demonstrate that the CRISPR/Cas12a assay is capable of effectively detecting the SARS-CoV-2 BA.2,BA.4,and BA.5 variants with a limit of detection of 10,1,and 10 copies/μL,respectively.Importantly,our assay successfully differentiated the three SARS-CoV-2 Omicron strains from one another.Additionally,we evaluated 46 SARS-CoV-2 positive clinical samples consisting of BA.2(n=20),BA.4(n=6),and BA.5(n=20)variants,and the sensitivity of our assay ranged from 90%to 100%,while the specificity was 100%.Discussion:This research presents a swift and reliable CRISPR-based method that may be employed to track the emergence of novel SARS-CoV-2 variants.展开更多
We analyzed variations in the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)genome during a flight-related cluster outbreak of coronavirus disease 2019(COVID-19)in Shenzhen,China,to explore the characteri...We analyzed variations in the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)genome during a flight-related cluster outbreak of coronavirus disease 2019(COVID-19)in Shenzhen,China,to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations(iSNVs)in a confined space.Thirty-three patients with COVID-19 were sampled,and 14 were resampled 3-31 days later.All 47 nasopharyngeal swabs were deep-sequenced.iSNVs and similarities in the consensus genome sequence were analyzed.Three SARS-CoV-2 variants of concern,Delta(n=31),Beta(n=1),and C.1.2(n=1),were detected among the 33 patients.The viral genome sequences from 30 Delta-positive patients had similar SNVs;14 of these patients provided two successive samples.Overall,the 47 sequenced genomes contained 164 iSNVs.Of the 14 paired(successive)samples,the second samples(T2)contained more iSNVs(median:3;95%confidence interval[95%CI]:2.77-10.22)than did the first samples(T1;median:2;95%CI:1.63-3.74;Wilcoxon test,P=0.021).38 iSNVs were detected in T1 samples,and only seven were also detectable in T2 samples.Notably,T2 samples from two of the 14 paired samples had additional mutations than the T1 samples.The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event.Intra-host diversity increased gradually with time,and new site mutations occurred in vivo without a population transmission bottleneck.Therefore,we could not determine the generational relationship from the mutation site changes alone.展开更多
基金support from the Innovation Team Project of Department of Education of Guangdong Province(No.2018KCXTD026)Guangdong Scientific and Technological Project(2019B1515120043,2020A151501612,2021A1515220109,2022B1515020093)+1 种基金Science and Technology Innovation Commission of Shenzhen(Grant No.KCXFZ20201221173413038)Longhua District Science and Innovation Commission Project Grants of Shenzhen(JCYJ201904).
文摘Coronavirus disease 2019(COVID-19)is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).The gold standard method for the diagnosis of SARS-CoV-2 depends on quantitative reverse transcription-polymerase chain reaction till now,which is time-consuming and requires expensive instrumentation,and the confirmation of variants relies on further sequencing techniques.Herein,we first proposed a robust technique-methodology of electrochemical CRISPR sensing with the advantages of rapid,highly sensitivity and specificity for the detection of SARS-CoV-2 variant.To enhance the sensing capability,gold electrodes are uniformly decorated with electro-deposited gold nanoparticles.Using DNA template identical to SARS-CoV-2 Delta spike gene sequence as model,our biosensor exhibits excellent analytical detection limit(50 fM)and high linearity(R2=0.987)over six orders of magnitude dynamic range from 100 fM to 10 nM without any nucleic-acid-amplification assays.The detection can be completed within 1 h with high stability and specificity which benefits from the CRISPR-Cas system.Furthermore,based on the wireless micro-electrochemical platform,the proposed biosensor reveals promising application ability in point-of-care testing.
基金Key projects of technology projects of Shenzhen Science and Technology Innovation Commission(JSGG20200225152648408).
文摘On January 22,2021,a 34-year-old male,who served as a security guard at the isolation point in Shenzhen,tested positive for coronavirus disease 2019(COVID-19)during the every-three-day routine test.After the nasopharyngeal swab was further confirmed as positive for COVID-19 by Shenzhen CDC,the patient was transferred to the Third People’s Hospital of Shenzhen and was diagnosed as a COVID-19 asymptomatic infection.On January 25,2021,Shenzhen CDC identified the 20H/501.Y.V2(B.1.351)variant,which was a variant of COVID-19 virus first emerging in the South Africa.
基金Shenzhen Science and Technology Innovation Commission Key project(no.JSGG20200225152648408)the Shenzhen Science and Technology Innovation Commission COVID-19 Special Fund(no.JSGG20200207161926465)Sanming Project of Medicine in Shenzhen(No.SZSM202011008).
文摘On June 14,2021,a customs officer(Case A)went to the infirmary at Baoan International Airport in Shenzhen due to a runny nose and fever.He was admitted to the Central Hospital of Baoan immediately.This patient preliminarily tested positive for coronavirus disease 2019(COVID-19)infection,caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),using a quantitative realtime reverse transcription polymerase chain reaction(qRT-PCR)method in this hospital.Then,a mixed specimen of nasopharyngeal swab.
基金Shenzhen Science and Technology Innovation Commission Key project(No.JSGG20200225152648408)the Shenzhen Science and Technology Innovation Commission COVID-19 Special Fund(No.JSGG20200207161926465)Sanming Project of Medicine in Shenzhen(No.SZSM202011008).
文摘Screening for coronavirus disease 2019(COVID-19)virus,also known as SARS-CoV-2,infection every seven days was performed for high-risk populations who worked at the Yantian Port in Yantian District,Shenzhen City,Guangdong Province.On May 20,2021,an oropharyngeal swab from a 44-year-old male(Case A)tested preliminarily positive for COVID-19 by a quantitative real-time reverse transcription polymerase chain reaction(RT-qPCR)method in a third-party laboratory.
基金The work was supported by grants from The Science Technology and Innovation Committee of Shenzhen Municipality[JCYJ20180507181627057 to M.-L.H.,JGSS20200225152648408,20220606141401003 to Y.H.]RGC General Research Fund of Hong Kong Special Administrative Region[11104020]and Strategic funds from City University of Hong Kong to M.-L.H.
文摘The coronavirus disease 2019(COVID-19)caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis,bringing enormous burden to our society.Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms.
基金Supported by the Key Project of Science and Technology(Grant No.2017ZX10104001-003)China-US Collaborative Program on Emerging and Re-emerging Infectious Disease(1U01GH 002224).
文摘Introduction:Human noroviruses are the leading cause of acute viral gastroenteritis(AGE)worldwide in all age groups.GII.4 strains have been the predominant genotype circulating globally over the last 2 decades and since 2012.GII.4 Sydney viruses have emerged and caused the majority of AGE outbreaks worldwide.Methods:Data from norovirus outbreaks from the laboratory-based surveillance of norovirus outbreaks in China(CaliciNet China)between October 2016–December 2020 were analyzed.Results:During October 2016–December 2020,1,954 norovirus outbreaks were reported,and positive fecal samples from 1,352(69.19%)outbreaks were genotyped.GII.4 Sydney[P31]viruses accounted for 2.1%(October 2016–August 2017),5.5%(September 2017–August 2018),3.3%(September 2018–August 2018),26.6%(September 2019–August 2020),and and 1.1%(September 2020–December 2020)of GII outbreaks,respectively.Compared to reference strains of GII.4 Sydney[P31]from 2012 to 2013,7 amino acid mutations in epitopes[A(297,372 and 373),B(333),E(414),and H(309 and 310)]and 1 in human histo-blood group antigens binding site at site II 372 were found by analyzing 9 GII.4 Sydney[P31]complete genomic sequences.Conclusions:This report identified the genomic variation of GII.4 Sydney[P31]from CaliciNet China.Continued surveillance with prompt genotyping and genetic analysis is necessary to monitor the emergence of novel GII.4 variants.
基金This work was supported by the National Key Research and Development Program of China 2022YFC0870700the Natural Science Foundation of China 92169201 and 82150710553,and Joint-Innovation Program in Healthcare for Special Scientific Research Projects of Guangzhou to H.Z+2 种基金This work was supported by the Natural Science Foundation of China,92169108 and 32000613 to Y.Z.the Shenzhen Science and Technology Innovation Commission Key project JSGG20200225152648408Special project for 2019-nCoV epidemic emergency prevention of the Shenzhen Science and Technology Innovation Commission JSGG20220606141401003 to Y.H.
文摘Dear Editor,The Omicron(B.1.1.529)variant of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)was first identified in November 2021,in South Africa and Botswana.The first Omicron sub-lineage that emerged was BA.1,which was supplanted by BA.2 in many countries.One of the most notable features of the Omicron variant is its ability to evade neutralizing antibodies(nAbs)targeting the original virus lineages.
基金Supported by the National Key Research and Development Program of China(2021YFC2300101,2021YFC0863300,2022YFC 2304101,2022YFC2303401).
文摘Introduction:Since 2019,numerous variants of concern for severe acute respiratory syndrome virus 2(SARS-CoV-2)have emerged,leading to significant outbreaks.The development of novel,highly accurate,and rapid detection techniques for these new SARSCoV-2 variants remains a primary focus in the ongoing efforts to control and prevent the coronavirus disease 2019(COVID-19)pandemic.Methods:Reverse transcription-recombinase polymerase amplification combined with the clustered regularly interspaced short palindromic repeatsassociated protein 12a(CRISPR/Cas12a)system was used to validate the detection of the Omicron BA.2,BA.4,and BA.5 variants of SARS-CoV-2.Results:Our results demonstrate that the CRISPR/Cas12a assay is capable of effectively detecting the SARS-CoV-2 BA.2,BA.4,and BA.5 variants with a limit of detection of 10,1,and 10 copies/μL,respectively.Importantly,our assay successfully differentiated the three SARS-CoV-2 Omicron strains from one another.Additionally,we evaluated 46 SARS-CoV-2 positive clinical samples consisting of BA.2(n=20),BA.4(n=6),and BA.5(n=20)variants,and the sensitivity of our assay ranged from 90%to 100%,while the specificity was 100%.Discussion:This research presents a swift and reliable CRISPR-based method that may be employed to track the emergence of novel SARS-CoV-2 variants.
基金the National Natural Science Foundation of China(grant number 82161148009)the Non‐profit Central Research Institute Fund of the Chinese Academy of Medical Science(grant number APL211276910010201002008)+4 种基金the Shenzhen Science and Technology Innovation Commission Key project(grant number JSGG20200225152648408)the Shenzhen Key Medical Discipline Construction Fund(grant number SZXK064)the Key Project of Shenzhen Science and Technology Innovation Commission(grant number KCXFZ2020020110061900)the First Fighting the Epidemic Project of Shenzhen(grant number JSGG 20210901145004012)the key project of Beijing Natural Science Foundation(grant number Z190017).
文摘We analyzed variations in the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)genome during a flight-related cluster outbreak of coronavirus disease 2019(COVID-19)in Shenzhen,China,to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations(iSNVs)in a confined space.Thirty-three patients with COVID-19 were sampled,and 14 were resampled 3-31 days later.All 47 nasopharyngeal swabs were deep-sequenced.iSNVs and similarities in the consensus genome sequence were analyzed.Three SARS-CoV-2 variants of concern,Delta(n=31),Beta(n=1),and C.1.2(n=1),were detected among the 33 patients.The viral genome sequences from 30 Delta-positive patients had similar SNVs;14 of these patients provided two successive samples.Overall,the 47 sequenced genomes contained 164 iSNVs.Of the 14 paired(successive)samples,the second samples(T2)contained more iSNVs(median:3;95%confidence interval[95%CI]:2.77-10.22)than did the first samples(T1;median:2;95%CI:1.63-3.74;Wilcoxon test,P=0.021).38 iSNVs were detected in T1 samples,and only seven were also detectable in T2 samples.Notably,T2 samples from two of the 14 paired samples had additional mutations than the T1 samples.The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event.Intra-host diversity increased gradually with time,and new site mutations occurred in vivo without a population transmission bottleneck.Therefore,we could not determine the generational relationship from the mutation site changes alone.
