Genomic Surveillance for SARS-CoV-2—China,September 26,2022 to January 29,2023

Introduction:The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has generated 2,431 variants over the course of its global transmission over the past 3 years.To better evaluate the genomic variation of SARS-CoV-2 before and after the optimization of coronavirus disease 2019(COVID-19)prevention and control strategies,we analyzed the genetic evolution branch composition and genomic variation of SARS-CoV-2 in both domestic and imported cases in China(the data from Hong Kong and Macao Special Administrative Regions and Taiwan,China were not included)from September 26,2022 to January 29,2023.Methods:Analysis of the number of genome sequences,sampling time,dynamic changes of evolutionary branches,origin,and clinical typing of SARS-CoV-2 variants submitted by 31 provincial-level administrative divisions(PLADs)and Xinjiang Production and Construction Corps(XPCC)was conducted to assess the accuracy and timeliness of SARS-CoV-2 variant surveillance.Results:From September 26,2022 to January 29,2023,20,013 valid genome sequences of domestic cases were reported in China,with 72 evolutionary branches.Additionally,1,978 valid genome sequences of imported cases were reported,with 169 evolutionary branches.The prevalence of the Omicron variants of SARS-CoV-2 in both domestic and imported cases was consistent with that of international epidemic variants.Conclusions:This study provides an overview of the prevalence of Omicron variants of SARS-CoV-2 in China.After optimizing COVID-19 prevention and control strategies,no novel Omicron variants of SARSCoV-2 with altered biological characteristics or public health significance have been identified since December 1,2022.

Epidemiology and genetic characteristics of coxsackievirus A16 associated with hand-foot-and-mouth disease in Yantai city,China in 2018-2021

In 2008,China launched a national surveillance system for hand‐foot‐and‐mouth disease(HFMD).Several million cases of HFMD are reported every year,coxsackievirus A16(CVA16)was the leading cause of HFMD epidemic in Yantai city,China in recent years,but the information of epidemiology and molecular characterization of CVA16 in Yantai is limited.The aim of this study is to investigate the epidemiological characteristics and pathogenic spectrum of HFMD,and most importantly,the molecular characterization of CVA16 in Yantai from 2018 to 2021.A total of 2,000 clinical samples were collected in Yantai city from 2018 to 2021 and the enterovirus typing was performed using real‐time reverse transcriptase–polymerase chain reaction(qRT‐PCR).VP1 coding regions of 41 CVA16 isolates were amplified and Sanger sequenced,and phylogenetic analysis was performed.During the study period,HFMD became prevalent from May to August each year.It peaked in June and declined in September.The incidence was highest in children aged 1 to 5 years,while more common in males than females.1,617 out of 2,000 clinical collection of samples were tested positive for enterovirus.Among them,614 were identified as CVA16,45 were enterovirus A71(EV A17),and 958 were other enterovirus serotypes.All 41 CVA16 strains belonged to the Bla and B1b genotypes.Homology analysis showed that 41 CVA16 isolates shared 83.2%–100%nucleotide and 93.7%–100%amino acid similarity among themselves.The results of this study update molecular epidemiology of CVA16 and provide a reference for HFMD prevention and control.

A novel human mAb (MERS-GD27) provides prophylactic and postexposure efficacy in MERS-CoV susceptible mice

Dear Editor,Since September 2012, the Middle East respiratory syndrome coronavirus (MERS-CoV) cases have been reported in more than 27 countries, and more than 2,000 cases have been confirmed in the laboratory (http://www.who.int/emergencies/mers-cov/en/). MERS-CoV causes an acute and severe respiratory illness with a high mortality rate(~35%) in humans (Shi et al., 2017, Zaki et al., 2012).Neutralizing antibodies targeting the spike of MERS-CoV have been shown to be a therapeutic option for treatment of lethal disease (Agrawal et al., 2016, Ying et al., 2014).

A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases--Wuhan,China 2019−2020

Emerging and re-emerging pathogens are great challenges to the public health(1).A cluster of pneumonia cases with an unknown cause occurred in Wuhan starting on December 21,2019.As of January 20,2020,a total of 201 cases of pneumonia in China have been confirmed.A team of professionals from the National Health Commission and China CDC conducted epidemiological and etiological investigations.On January 3,2020,the first complete genome of the novelβgenus coronaviruses(2019-nCoVs)was identified in samples of bronchoalveolar lavage fluid(BALF)from a patient from Wuhan by scientists of the National Institute of Viral Disease Control and Prevention(IVDC)through a combination of Sanger sequencing,Illumina sequencing,and nanopore sequencing.Three distinct strains have been identified,the virus has been designated as 2019-nCoV,and the disease has been subsequently named novel coronavirus-infected pneumonia(NCIP).

Development of an innovative one-step nested PCR strategy for virus detection using the LNA technique

Dear Editor,Polymerase chain reaction(PCR)is a molecular diagnostic technique that has been widely used for diagnosing viral diseases.Nested PCR(N-PCR)is a variation on the standard PCR technique that involves two amplification steps,yielding greater sensitivity and specificity.But there are two main disadvantages:the protocol is more complex than conventional PCR,and the risk of cross-contamination is relatively high.One-step nested PCR(OSN-PCR)enables conventional N-PCR to be performed as a closed reaction in a single tube that contains both outer and inner primers.This strategy makes OSN-PCR more rapid than N-PCR,lowers the probability of cross-contamination,and requires a smaller amount of reagents.

Two-tube multiplex real-time reverse transcription PCR to detect six human coronaviruses

Dear Editor,Coronaviruses are enveloped positive-strand RNA viruses with 27–33 kb genomes.These viruses are classified into four genera,namely Alphacoronavirus,Betacoronavirus,Gammacoronavirus,and

COVID-19 Outbreak Caused by Contaminated Packaging of Imported Cold-Chain Products—Liaoning Province,China,July 2020

Summary What is known about this topic?Few major outbreaks of coronavirus disease 2019(COVID-19)have occurred in China after major nonpharmaceutical interventions and vaccines have been deployed and implemented.However,sporadic outbreaks that had high possibility to be linked to cold chain products were reported in several cities of China..What is added by this report?In July 2020,a COVID-19 outbreak occurred in Dalian,China.The investigations of this outbreak strongly suggested that the infection source was from COVID-19 virus-contaminated packaging of frozen seafood during inbound unloading personnel contact.What are the implications for public health practice?Virus contaminated paper surfaces could maintain infectivity for at least 17–24 days at-25℃.Exposure to COVID-19 virus-contaminated surfaces is a potential route for introducing the virus to a susceptible population.Countries with no domestic transmission of COVID-19 should consider introducing prevention strategies for both inbound travellers and imported goods.Several measures to prevent the introduction of the virus via cold-chain goods can be implemented.

Eleven COVID-19 Outbreaks with Local Transmissions Caused by the Imported SARS-CoV-2 Delta VOC-China,July-August,2021

Starting from December 2019,Wuhan,China,encountered the first outbreak of coronavirus disease 2019(COVID-19)(1-2).The epidemic was successfully suppressed by strict containment so that the number of infected people was reduced to 0 on April 8,2020(3–4).After that,China experienced roughly 3 dozen outbreaks with local transmission caused by imported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).

A core-shell structured COYID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity

Although inoculation of COVID-19 vaccines has rolled out globally,there is still a critical need for safe and effective vaccines to ensure fair and equitable supply for all countries.Here,we report on the development of a highly efficacious mRNA vaccine,SW0123 that is composed of sequence-modified mRNA encoding the full-length SARS-CoV-2 Spike protein packaged in core-shell structured lipopolyplex(LPP)nanoparticles.SWOT 23 is easy to produce using a large-scale microfluidics-based apparatus.The unique core-shell structured nanoparticle facilitates vaccine uptake and demonstrates a high colloidal stability,and a desirable biodistribution pattern with low liver targeting effect upon intramuscular administration.Extensive evaluations in mice and nonhuman primates revealed strong immunogenicity of SW0123,represented by induction of Th1-polarized T cell responses and high levels of antibodies that were capable of neutralizing not only the wild-type SARS-CoV-2,but also a panel of variants including D614G and N501Y variants.In addition,SW0123 conferred effective protection in both mice and non-human primates upon SARS-CoV-2 challenge.Taken together,SW0123 is a promising vaccine candidate that holds prospects for further evaluation in humans.

Three Novel Real-Time RT-PCR Assays for Detection of COVID-19 Virus

What is already known on this topic?A novel human coronavirus,known as SARS-CoV-2 or 2019-nCoV,is the causative agent of the coronavirus disease 2019(COVID-19).We have released the primers and probes of real-time reverse transcription polymerase chain reaction(rRT-PCR)assays for the laboratory detection of COVID-19 infection.What is added by this report?Here we provide detailed technical data and evaluate the performance of three novel rRT-PCR assays targeting the ORF1ab,N,and E genes for detection of COVID-19 infection.The application of rRT-PCR assays among four types of specimens(alveolar lavage,sputum,throat swabs,and stool)from patients with COVID-19 indicated that the mean viral loads detected in sputum were higher than other specimens.What are the implications for public health practice?These rRT-PCR assays reported here could be used for laboratory diagnosis of COVID-19 infection with high sensitivity,specificity,and applicability.Sputum rather than throat swabs and stool should be a priority for specimen collection for laboratory detection of COVID-19.

Reemergent Cases of COVID-19—Xinfadi Wholesales Market,Beijing Municipality,China,June 11,2020

No new local coronavirus disease 2019(COVID-19)cases were reported in Beijing for over 56 days before the reemergent COVID-19 cases that were reported on June 11,2020,and more than 200 confirmed cases have been reported as of June 20 in Beijing.All confirmed COVID-19 cases were associated with Xinfadi Wholesale Market.Here,we reported the phylogenetic characteristics of the COVID-19 viruses(also known as severe acute respiratory syndrome coronavirus 2,SARS-CoV-2,and human coronavirus 2019,HCoV-19)sequenced from the clinical specimens of 2 human cases and 1 environmental sample.

Genetic tracing of HCoV-19 for the re-emerging outbreak of COVID-19 in Beijing, China

The ongoing pandemic of coronavirus disease 2019(COVID-19)caused by a novel severe acute respiratory syndrome coronavirus 2(SARS-CoV-2,also named as 2019-nCoV or HCoV-19)poses an unprecedented threat to public health(Zhu et al.,2020;Wang et al.,2020;Jiang et al.,2020).The novel HCoV-19 virus has rapidly spread into multiple countries across the world since it was first reported in December 2019.The World Health Organization(WHO)declared COVID-19 as a pandemic on 11th March 2020.As of 4th July,over 10 million confirmed COVID-19 cases have been reported in over 200 countries/regions with more than 0.5 million deaths,including 85,287 documented cases and 4,648 deaths in China(WHO,2020a).

A novel luciferase immunosorbent assay performs better than a commercial enzyme-linked immunosorbent assay to detect MERS-CoV specific IgG in humans and animals

The Middle East respiratory syndrome(MERS)is a lethal zoonosis caused by MERS coronavirus(MERS-CoV)and poses a significant threat to public health worldwide.Therefore,a rapid,sensitive,and specific serologic test for detecting anti-MERS-CoV antibodies in both humans and animals is urgently needed for the successful management of this illness.Here,we evaluated various novel luciferase immunosorbent assays(LISA)based on nucleocapsid protein(NP)as well as fragments derived from spike protein(S)including subunit 1(S1),N terminal domain(NTD),receptorbinding domain(RBD)and subunit 2(S2)of S for the detection of MERS-CoV-specific IgG.Fusion proteins,including nanoluciferase(NLuc)and various fragments derived from the NP or S protein of MERS-CoV,were expressed in human embryonic kidney 293 T cells.LISAs that detected anti-MERS-CoV IgG were further developed using cell lysates expressing various fusion proteins.Panels of human or animal samples infected with MERS-CoV were used to analyze the sensitivity and specificity of various LISAs in reference to a MERS-CoV RT-PCR,commercial S1-based ELISA,and pseudovirus particle neutralization test(ppNT).Our results showed that the S1-,RBD-,and NP-LISAs were more sensitive than the NTD-and S2-LISAs for the detection of anti-MERS-CoV IgG.Furthermore,the S1-,RBD-,and NP-LISAs were more sensitive(by at least 16-fold)than the commercially available S1-ELISA.Moreover,the S1-,RBD-,and NPLISA specifically recognized anti-MERS-CoV IgG and did not cross-react with samples derived from other human CoV(OC43,229E,HKU1,NL63)-infected patients.More importantly,these LISAs proved their applicability and reliability for detecting anti-MERS-CoV IgG in samples from camels,monkeys,and mice,among which the RBD-LISA exhibited excellent performance.The results of this study suggest that the novel MERS-CoV RBD-and S1-LISAs are highly effective platforms for the rapid and sensitive detection of anti-MERS-CoV IgG in human and animal samples.These assays have the potential to be used as serologic tests for the management and control of MERS-CoV infection.

Genomic Surveillance for SARS-CoV-2 Variants of Concern from Imported COVID-19 Cases-the Mainland of China,2021

Introduction:After the epidemic in Wuhan City was brought under control in 2020,local outbreaks of coronavirus disease 2019(COVID-19)in the mainland of China were mainly due to imported COVID-19 cases.The ongoing evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has continued to generate new variants.Some have been designated as variants of concern(VOCs)by the World Health Organization(WHO).To better assess the role of imported SARS-CoV-2 surveillance and the prevalence of VOCs in 2021,the genomic surveillance data of SARS-CoV-2 from imported COVID-19 cases of 2021 in the mainland of China were analyzed.Methods:The analyses included the number of sequence submissions,time of sequence deposition,and time of detection of the VOCs in order to determine the timeliness and sensitivity of the surveillance.The proportions of VOCs were analyzed and compared with data from the Global Initiative of Sharing All Influenza Data(GISAID).Results:A total of 3,355 sequences of imported cases were submitted from 29 provincial-level administrative divisions,with differences in the number of sequence submissions and median time of sequence deposition.A total of 2,388 sequences with more than 90%genomic coverage were used for lineage analysis.The epidemic trend from Alpha to Delta to Omicron in imported cases was consistent with that in the GISAID.In addition,VOCs from imported cases were usually identified after WHO designation and before causing local outbreaks.Conclusions:The global distribution of SARSCoV-2 VOCs changed rapidly in 2021.Robust genomic surveillance of the imported SARS-CoV-2 in the mainland of China is of great significance.Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),is constantly mutating under the different circumstances of global transmission(1).The emerging SARS-CoV-2 variants may have potential adverse impacts on epidemic traits and severity.To some extent,it is also capable of escaping natural and vaccine-induced immunity(2–3).Some of them were designated as variants of concern(VOCs)by the World Health Organization(WHO)(4).Therefore,robust surveillance is essential to assess the evolution of viruses in real time.After the epidemic in Wuhan City was brought under control in 2020,several COVID-19 outbreaks in the mainland of China have been proven to relate to SARS-CoV-2 contaminated cold-chain products(5–7),while most were caused by transmission through imported cases on flights,at isolation facilities,or in designated hospitals(8–9).Therefore,genomic surveillance for SARS-CoV-2 from imported cases is of great significance for monitoring the risk of different variants that were imported into the mainland of China,assessing the risk of importation-associated domestic spread,and helping guide public health interventions.On March 17,2020,the China CDC released a notice and launched genomic surveillance for SARS-CoV-2 from imported COVID-19 cases nationwide.The laboratories of provincial CDCs were required to conduct SARS-CoV-2 whole-genome sequencing for samples from imported cases and submit the genomic sequences to the China CDC in time.This study includes the analysis of genomic surveillance data of imported SARS-CoV-2 cases of 2021 from the mainland of China.

Surveillance and Analysis of SARS-CoV-2 Variant Importation—China,January–June 2022

Introduction:The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)Omicron variant is the dominant circulating strain worldwide.To assess the importation of SARS-CoV-2 variants in the mainland of China during the Omicron epidemic,the genomic surveillance data of SARS-CoV-2 from imported coronavirus disease 2019(COVID-19)cases in the mainland of China during the first half of 2022 were analyzed.Methods:Sequences submitted from January to July 2022,with a collection date before June 30,2022,were incorporated.The proportions of SARS-CoV-2 variants as well as the relationships between the origin and destination of each Omicron imported case were analyzed.Results:4,946 sequences of imported cases were submitted from 27 provincial-level administrative divisions(PLADs),and the median submission interval was within 1 month after collection.In 3,851 Omicron sequences with good quality,1 recombinant(XU)and 4 subvariants under monitoring(BA.4,BA.5,BA.2.12.1,and BA.2.13)were recorded,and 3 of them(BA.4,BA.5,and BA.2.12.1)caused local transmissions in the mainland of China later than that recorded in the surveillance.Omicron subvariants dominated in the first half of 2022 and shifted from BA.1 to BA.2 then to BA.4 and BA.5.The percentage of BA.2 in the imported SARS-CoV-2 surveillance data was far higher than that in the Global Initiative on Sharing All Influenza Data(GISAID).The imported cases from Hong Kong Special Administrative Region,China,accounted for 32.30%of Omicron cases sampled,and 98.71%of them were BA.2.Conclusions:The Omicron variant showed the intra-Omicron evolution in the first half of 2022,and all of the Omicron subvariants were introduced into the mainland of China multiple times from multiple different locations.

Profiles of SARS-CoV-2 RNA and Antibodies in Inpatients with COVID-19 not Related with Clinical Manifestation: A Single Centre Study

Dear Editor,A novel coronavirus disease(COVID-19)caused by acute respiratory syndrome coronavirus 2(SARS-Co V-2)first broke out in Wuhan,Hubei Province,China,in 2019.More than 50 million cases of COVID-19 have been confirmed globally with 1,280,868 deaths reported as of November12,2020(https://covid19.who.int/).

Genome Characterization of COVID-19 Lineage B.1.1.7 Detected in the First Six Patients of a Cluster Outbreak——Shenzhen City,Guangdong Province,China,May 2021

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.

Sequencing the Complete Genome of COVID-19 Virus from Clinical Samples Using the Sanger Method

What is already known on this topic?Coronavirus disease 2019(COVID-19),a disease caused by a novel human coronavirus named the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)or COVID-19 virus,was reported in December 2019.Complete genomes of the COVID-19 virus from clinical samples using next generation sequencing(NGS)have been reported.What is added by this report?Here we provide the technical data for sequencing complete genome of COVID-19 virus from clinical samples using the Sanger method.Two complete COVID-19 virus genome sequences(named WH19004-S and GX0002)were obtained from clinical samples of COVID-19 patients,and two single nucleotide polymorphisms(SNPs)in ORF7a(T/C,nt 27,493)and ORF8(T/C,nt 28,253)of WH19004-S were identified by Sanger sequencing.What are the implications for public health practice?The COVID-19 virus genome sequencing by Sanger method reported here could be used to generate data of high enough quality without requirement for expensive NGS equipment,which support sequencing complete genomes from clinical samples and monitoring of viral genetic variations of COVID-19 infections.