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.

Functional and structural characterization of Norovirus GII.6 in recognizing histo-blood group antigens

Noroviruses(NoVs)are the primary cause of acute gastroenteritis worldwide.Histo-blood group antigens(HBGAs)are receptors or attachment factors that affect the prevalence and host susceptibility of NoVs.GII.6 NoV is one of the predominant genotypes in humans,which recognizes the type ABO secretor of HBGAs.However,the structural basis of GII.6 NoV's interaction with HBGAs receptors remains elusive.In this study,we investigated the binding features of the GII.6 strain to HBGAs using saliva-and glycan-ELISA assays and characterized the molecular basis of the GII.6 virus that recognizes H disaccharide.We showed that the GII.6 P domain recognized some A and O secretor's saliva samples,most B secretor's saliva samples,and H disaccharide antigen,but did not bind non-secretors’saliva.Further,we determined the crystal structures of GII.6 and its complex with H disaccharides at 1.7Å,revealing that the P domain of GII.6 shares the conventional binding interface and mode of GII HBGAs.Single residue mutations at the GII.6-H binding sites could inhibit the binding of GII.6 to HBGAs,demonstrating that the interaction residues were crucial in maintaining NoV-glycan integrity.Finally,structural and sequence analyses showed that the major residues of the GII.6-H interaction were conserved among NoVs in the GII genogroup.Taken together,our study characterized the functional and structural features of GII.6 that allow it to interact with HBGAs,and shed light on NoV evolution,epidemiology,and anti-viral drug development.

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.

Epidemiological and virological surveillance of influenza viruses in China during 2020–2021

Background: During the coronavirus disease 2019(COVID-19)pandemic,seasonal influenza activity declined globally and remained below previous seasonal levels,but intensified in China since 2021.Preventive measures to COVID-19 accompanied by different epidemic characteristics of influenza in different regions of the world.To better respond to influenza outbreaks under the COVID-19 pandemic,we analyzed the epidemiology,antigenic and genetic characteristics,and antiviral susceptibility of influenza viruses in the mainland of China during 2020–2021.Methods: Respiratory specimens from influenza like illness cases were collected by sentinel hospitals and sent to network laboratories in Chinese National Influenza Surveillance Network.Antigenic mutation analysis of influenza virus isolates was performed by hemagglutination inhibition assay.Next-generation sequencing was used for genetic analyses.We also conducted molecular characterization and phylogenetic analysis of circulating influenza viruses.Viruses were tested for resistance to antiviral medications using phenotypic and/or sequence-based methods.Results: In the mainland of China,influenza activity recovered in 2021 compared with that in 2020 and intensified during the traditional influenza winter season,but it did not exceed the peak in previous years.Almost all viruses isolated during the study period were of the B/Victoria lineage and were characterized by genetic diversity,with the subgroup 1A.3a.2 viruses currently predominated.37.8%viruses tested were antigenically similar to reference viruses representing the components of the vaccine for the 2020–2021 and 2021–2022 Northern Hemisphere influenza seasons.In addition,China has a unique subgroup of 1A.3a.1 viruses.All viruses tested were sensitive to neuraminidase inhibitors and endonuclease inhibitors,except two B/Victoria lineage viruses identified to have reduced sensitivity to neuraminidase inhibitors.Conclusions: Influenza activity increased in the mainland of China in 2021,and caused flu season in the winter of 2021–2022.Although the diversity of influenza(sub)type decreases,B/Victoria lineage viruses show increased genetic and antigenic diversity.The world needs to be fully prepared for the co-epidemic of influenza and severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)virus globally.

The Functional Characterization of Bat and Human P[3] Rotavirus VP8*s

P[3]rotavirus(RV)has been identified in many species,including human,simian,dog,and bat.Several glycans,including sialic acid,histo-blood group antigens(HBGAs)are reported as RV attachment factors.The glycan binding specificity of different P[3]RV VP8*s were investigated in this study.Human HCR3 A and dog P[3]RV VP8*s recognized glycans with terminal sialic acid and hemagglutinated the red blood cells,while bat P[3]VP8*showed neither binding to glycans nor hemagglutination.However,the bat P[3]VP8*mutant of C189 Y obtained the ability to hemagglutinate the red blood cells,while human P[3]HCR3 A/M2-102 mutants of Y189 C lost the ability.Sequence alignment and structural analysis indicated that residue 189 played an important role in the ligand recognition and may contribute to the cross-species transmission.Structural superimposition exhibited that bat P[3]VP8*model was quite different from the simian P[3]Rhesus rotavirus(RRV)P[3]VP8*,indicating that bat P[3]RV was relatively distinct and partially contributed to the no binding to tested glycans.These results promote our understanding of P[3]VP8*/glycans interactions and the potential transmission of bat/human P[3]RVs,offering more insight into the RV infection and prevalence.

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.

Reemergent Cases of COVID-19--Xinjiang Uygur Autonomous Region,China,July 16,2020

Before the coronavirus disease 2019(COVID-19)outbreak on July 16,2020,no new COVID-19 cases were reported in Urumqi City of Xinjiang for 150 consecutive days.During this outbreak,826 confirmed COVID-19 cases have been reported in Urumqi.The phylogenetic characteristics of COVID-19 virus from clinical specimens of the initial 4 cases in the Urumqi outbreak were sequenced.

Structural Basis of Glycan Recognition in Globally Predominant Human P[8]Rotavirus

Rotavirus(RV)causes acute gastroenteritis in infants and children worldwide.Recent studies showed that glycans such as histo-blood group antigens(HBGAs)function as cell attachment factors affecting RV host susceptibility and prevalence.P[8]is the predominant RV genotype in humans,but the structural basis of how P[8]RVs interact with glycan ligands remains elusive.In this study,we characterized the interactions between P[8]VP8~*s and glycans which showed that VP8~*,the RV glycan binding domain,recognized both mucin core 2 and H type 1 antigens according to the ELISA-based oligosaccharide binding assays.Importantly,we determined the structural basis of P[8]RV-glycans interaction from the crystal structures of a Rotateq P[8]VP8~*in complex with core 2 and H type 1 glycans at 1.82.3?,respectively,revealing a common binding pocket and similar binding mode.Structural and sequence analysis demonstrated that the glycan binding site is conserved among RVs in the P[Ⅱ]genogroup,while genotype-specific amino acid variations determined different glycan binding preference.Our data elucidated the detailed structural basis of the interactions between human P[8]RVs and different host glycan factors,shedding light on RV infection,epidemiology,and development of anti-viral agents.

The Initial Case of COVID-19—Shulan City,Jilin Province,China,May 8,2020

Coronavirus disease 2019(COVID-19)was designated a global pandemic by the World Health Organization(WHO)on March 11,2020(1).After great effort,COVID-19 has been well-controlled in China,but new challenges have emerged due to increasing numbers of imported cases from outside of China.On May 8,the Health Commission of Jilin Province reported a confirmed COVID-19 case of a 45-year-old laundry woman from Shulan City in the northeast of China.This case was suspected to be associated with a possible importation event.