IntroductionNorovirus is a key pathogen of acute gastroenteritis and poses a significant burden on both the economy and public health. This study focuses on continuous monitoring of norovirus in Shenzhen, China, from 2016 to 2022, aiming to analyze the epidemic characteristics and genetic diversity of norovirus in the context of global sequence data.MethodsThe study was based on data collected from local sentinel hospitals. It involved analyzing the demographic, spatial, and temporal distribution of norovirus infections. Phylogenetic analysis was conducted, and genotype dynamics were compared across geographic levels. Mutations affecting protein stability were evaluated, and recombination analysis was performed to identify critical breakpoints and fragments for norovirus.ResultsThe study found that norovirus primarily infected infants under 3 years old, with epidemics occurring in winter and concentrated in developed districts. Phylogenetic analysis revealed both similarities and differences in the evolutionary patterns of various genotypes at different geographical levels. Mutations in the VP1 protein, based on the protein structure of GII.4_Sydney[P31], provided insights into the evolutionary trends of key genotypes. Additionally, recombination analysis identified important breakpoints and fragments for norovirus.DiscussionThe findings offer valuable insights to evolution and transmission of norovirus. These results can serve as a reference for future research, and they may aid in vaccine development efforts aimed at controlling norovirus outbreaks.

Inositol hexakisphosphate (IP6) promotes HIV-1 assembly by stabilizing the immature Gag lattice and becomes enriched within virions, where it is required for mature capsid assembly. Previously, we identified Gag mutants that package little IP6 yet assemble particles, though they are non-infectious due to defective capsid formation. Here, we report a compensatory mutation, G225R, in the C-terminus of capsid protein (CA) that restores capsid assembly and infectivity in these IP6-deficient mutants. G225R also enhances in vitro assembly of CA into capsid-like particles at far lower IP6 concentrations than required for wild-type CA. CryoEM structures of G225R CA hexamers and lattices at 2.7 Å resolution reveal that the otherwise disordered C-terminus becomes structured, stabilizing hexamer-hexamer interfaces. Molecular dynamics simulations support this mechanism. These findings uncover how HIV-1 can adapt to IP6 deficiency and highlight a previously unrecognized structural role of the CA C-terminus, while offering tools for capsid-related studies.

BACKGROUND:Coinfections involving multiple diarrheal viruses have gained increasing recognition as a significant cause of acute gastroenteritis in recent years. Understanding the genetic diversity and evolutionary relationships of these viruses is crucial for effective outbreak identification and tracking. OBJECTIVE:To report two cases of HAdV and SaV coinfections and elucidate the genetic diversity and evolutionary patterns of these viruses through whole-genome sequencing (WGS) and phylogenetic analysis. METHODS:A total of 873 diarrheal stool samples were collected from sentinel hospitals in Shenzhen, China, in 2021. The collected stool samples were identified using RT-PCR and positive samples were subjected to WGS on the NovaSeq platform. phylogenetic trees were constructed using MEGA to analyze genetic relationships. RESULTS:The sequencing results showed that both samples were human adenovirus type 41, which clustered in two distinct evolutionary clades. Additionally, we also retrieved the complete genome of sapovirus (GI.1 genotype) from the same sample. Phylogenetic analysis revealed that they were similar to previously reported strains, belonging to the clade predominating in China. CONCLUSIONS:This study reveals the genetic diversity of epidemic strains involved in coinfections of human adenovirus and sapovirus. The findings establish a groundwork for the identification and traces of acute gastroenteritis outbreaks.

OBJECTIVES:To investigate the etiological characteristics of acute conjunctivitis in Shenzhen, China. METHODS:A total of 1234 conjunctival swabs collected between 2018 and 2024 were examined for coxsackievirus A24 variant (CVA24v), enterovirus D70 (EV-D70) and human adenovirus (HAdV). Complete VP1 sequences of CVA24v strains were determined and analyzed. HAdV was genotyped by PCR methods targeting the three genes (penton base, hexon and fiber) and sequencing. SPSS 22.0 software was used for statistical analysis. RESULTS:CVA24v was first detected in 2023, with a detection rate of 33.3 % (63/189). No EV-D70 was detected in 2018-2024. The annual distributions of HAdV-infected patients were 52.6 % (101/192), 62.7 % (111/177), 21.1 % (37/175), 9.0 % (14/155), 10.5 % (17/162), 15.9 % (30/189) and 21.7 % (40/184), respectively. CVA24v strains from this study clustered in a clade with significant temporal aggregation characteristic within the genotype GIV. Eight amino acid variation sites (T11A, I16L, K20I, L32P, K105R, A146T, R277G and P280S) were observed in VP1 sequences of CVA24v strains from this study when compared to the close strains. Conjunctivitis patients with one of the three symptoms (weakness, fever and blurred vision) had a higher detection rate of HAdV. Eleven known HAdV genotypes (HAdV-B3, -B14, -B21, HAdV-D8, -D37, -D42, -D53, -D64, -D85, -D115 and HAdV-E4) and 7 unknown genotypes were detected in 2020-2024, with HAdV-D37 (30.9 %), HAdV-D115 (21.1 %) and HAdV-B3 (17.1 %) being the three predominant genotypes. CONCLUSIONS:The unique genetic characteristics were observed in Shenzhen CVA24v strains. HAdVs associated with conjunctivitis exhibited a high degree of genotypic diversity in Shenzhen, and HAdV-D115 related to conjunctivitis was first reported in this study.

The study aimed to investigate epidemiological profile and molecular characteristics of coxsackievirus A10 (CVA10) associated with hand, foot and mouth disease (HFMD) in Shenzhen, China and comparatively analyze genomes of CVA10 strains related to differential clinical phenotypes. A total of 3170 clinical specimens collected between 2021 and 2024 were examined for CVA10 using real-time RT-PCR. Complete VP1 sequences and near-complete genome sequences of CVA10 were determined by RT-PCR methods and sequencing. Sequences were analyzed using a series of bioinformatics programs. Two (33.33%) out of 6 severe cases were infected with CVA10. The detection rate of CVA10 associated with mild HFMD ranged from 1.21% to 6.11% in 2021-2024, with an overall detection rate of 3.73%. There was no significant difference in the infection rate of CVA10 between males and females or different age groups. The CVA10 infections mainly occurred in Spring (March to May) and Summer (June to August) in Shenzhen. Of the 74 VP1 sequences determined, 71 (95.95%) of them were detected in the sub-genotype C2, 3 (4.05%) were assigned to the genotype D. Genomic sequence analysis indicated that the genotype D of CVA10 of this study derived from genetic recombination between CVA10 and CVA16 in 3A-3D coding region (nucleotide position: 5075-6896). Different variable sites were observed in the two CVA10 strains associated with different severe complications when compared to CVA10 strains associated with mild diseases. In conclusion, CVA10 associated with HFMD circulated at a low level in Shenzhen in 2021-2024, with C2 as the predominant genotype. Recombinant genotype D of CVA10 was introduced first to Shenzhen in 2024. The study emphasizes the importance of continuous molecular surveillance of CVA10.

In recent years, with the increasing demand for high-precision displays, Mini light-emitting diodes (Mini LED), as an important component of displays, have relatively high quality requirements for their production. However, various defects are inevitable during the production process. Therefore, the detection of product defects becomes crucial. Due to the complex texture of the Mini LED substrate and the diverse defect forms, with significant differences in shape, angle, and scale, traditional manual detection is inefficient and has limited accuracy, while conventional classification or object detection networks are difficult to effectively deal with such geometric deformations, and the object detection level box is difficult to fit the complete shape of the defect. In response to these, we propose the SD-YOLOv8 rotated object detection method based on YOLOv8, which is specifically designed for the defect detection task of Mini LED. To enhance the detection capability of small object defects, we add a small object detection head to the shallow layerularly rotating objects, and in order to enhance the feature extraction capability for defects of irregin the neck part, we integrate deformable convolutional on the Cross Stage Partial (CSP) bottleneck with 2 Convolutions (C2f) module in the neck part. Adaptive sampling of the rotation and deformation regions is achieved by using learnable offset and modulation factors. In addition, a oriented bounding box (OBB) detection head is adopted to predict the object position and rotation angle more accurately. The experimental results based on the self-built Mini LED defect dataset show that our model’s mAP50 reaches 96.7%, which is 2.3% higher than the baseline YOLOv8-OBB. The results verify that SD-YOLOv8 has superior performance of high precision and high efficiency in the industrial inspection scenarios of Mini LED.

Diarrhea is one of the major public health issues worldwide. Although the infections of individual enteric virus have been extensively studied, elucidation of the coinfection involving multiple viruses is still limited. In this study, we identified the coinfection of human adenovirus (HAdV) and human astrovirus (HAstV) in a child with acute gastroenteritis, analyzed their genotypes and molecular evolution characteristics. The sample was collected and identified using RT-PCR and subjected to whole-genome sequencing on the NovaSeq (Illumina) platform. Obtained sequences were assembled into the complete genome of HAdV and the ORF1 of HAstV. We conducted phylogenetic analysis using IQ-TREE software and conducted recombination analysis with the Recombination Detection Program. The sequenced HAdV was confirmed to be genotype 41, and was genetically close to some European strains. Phylogenetic analysis revealed that the HAstV was genetically close to both HAstV-2 and HAstV-4 and was different from the genotype prevalent in Shenzhen before. The recombination analysis confirmed that the sequenced HAstV strain is a recombinant of HAstV-2 and HAstV-4. Our analysis has shown that the strains in this coinfection are both uncommon variants in this geographical region, instead of dominant subtypes that have prevailed for years. This study presents a coinfection of HAdV and HAstV and conducts an evolutionary analysis on involved viruses, which reveals the genetic diversity of epidemic strains in Southern China and offers valuable insights into vaccine and medical research.

Combining bioinformatics and in vitro cytology assays, a predictive method was established to quickly evaluate the protective effect of immunity acquired through SARS-CoV-2 infection against variants. Bioinformatics software was first used to predict the changes in the affinity of variant antigens to the CV30 monoclonal antibody by integrating bioinformatics and cytology assays. Then, the ability of the antibody to neutralize the variant antigen was further verified, and the ability of the CV30 to neutralize the new variant strain was predicted through pseudovirus neutralization experiments. The current study has demonstrated that when the Molecular Operating Environment (MOE) predicts |ΔBFE| ≤ 3.0003, it suggests that the CV30 monoclonal antibody exhibits some affinity toward the variant strain and can potentially neutralize it. However, if |ΔBFE| ≥ 4.1539, the CV30 monoclonal antibody does not display any affinity for the variant strain and cannot neutralize it. In contrast, if 3.0003 < |ΔBFE| < 4.1539, it is necessary to conduct a series of neutralization tests promptly with the CV30 monoclonal antibody and the variant pseudovirus to obtain results and supplement the existing method, which is faster than the typical procedures. This approach allows for a rapid assessment of the protective efficacy of natural immunity gained through SARS-CoV-2 infection against variants.

This study focuses on maternal antibody transfer following vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before or during early pregnancy and its potential protective effects on infants, providing scientific evidence for vaccination strategies. This prospective study tested the samples for SARS-CoV-2 IgG antibody titers and neutralizing capacity and tracked the infections after birth. Perform multivariate analysis of factors influencing antibody transfer rate, newborn antibody titers, and infant infection. Total 87.1% (122/140) women received coronavirus disease 2019 (COVID-19) vaccine before or during early pregnancy, and 28 of them had breakthrough infection. The maternal and neonatal IgG positive rates at delivery were 60.7% (85/140) and 60.8% (87/143), respectively. A positive correlation was found between neonatal and maternal IgG antibody titers. Compared with the median IgG antibody transfer rate of infected pregnant women, that of vaccinated but not infected pregnant women was higher (1.21 versus: 1.53 [two doses], 1.71 [three doses]). However, neonatal IgG antibodies were relatively low (174.91 versus: 0.99 [two doses], 8.18 [three doses]), and their neutralizing capacity was weak. The overall effectiveness of maternal vaccination in preventing infant infection was 27.0%, and three doses had higher effectiveness than two doses (64.3% vs. 19.6%). Multivariate analysises showed that in vaccination group women receiving three doses or in infection group women with longer interval between infection and delivery had a higher antibody transfer rate and neonatal IgG antibody titer. More than half of women vaccinated before or during early pregnancy can achieve effective antibody transfer to newborns. However, the neonatal IgG antibody titer is low and has a weak neutralizing capacity, providing limited protection to infants.

Relay of information from the extracellular environment into the cell often results from a peptide growth factor binding to its cognate cell surface receptor; this event is an integral mechanism by which many cellular functions occur, including cell growth, motility, and survival. In recent years, however, this requirement for ligand binding has been shown to be surpassed by several distinct mechanisms, including cell surface receptor cross-talk (e.g., between epidermal growth factor receptor [EGFR] and G-coupled receptors), receptor-extracellular matrix interactions (e.g., EGFR: integrin complexes), and finally by structural mutations within the receptor itself. While all of these pathways result in so-called ligand-independent signaling by the EGF receptor, to date, only structural mutations in the receptor have been shown to result in qualitative changes in downstream targets of the receptor, which specifically result in oncogenic signaling, transformation, and tumorigenicity. In this review, we describe aspects of the known signaling properties of the retroviral oncogene v-ErbB as a model of ligand-independent oncogenic signaling, and compare these properties to results emerging from ongoing studies on structurally related EGF receptor mutants originally identified in human tumors. A better understanding of the signaling pathways used by these uniquely oncogenic receptor tyrosine kinase mutants may ultimately reveal new targets for the development of novel therapeutics selective for the inhibition of tumor cell growth.

Some children infected with hand, foot, and mouth disease (HFMD) caused by enterovirus 71 (EV71) progressed to severe disease with various neurological complications in the short term, with a poor prognosis and high mortality. Studies had revealed that RNA N 6 ‐methyladenosine (m 6 A) modification had a significant impact on EV71 replication, but it was unknown how m 6 A modification regulated the host cell's innate immune response brought on by EV71 infection. We used MeRIP‐seq (methylation RNA immunoprecipitation sequencing), RNA‐seq (RNA sequencing), cell transfection, and other techniques. MeRIP‐seq and RNA‐seq results showed the m 6 A methylation modification map of control and EV71‐infected groups of RD cells. And multilevel validation indicated that decreased expression of demethylase FTO (fat mass and obesity‐associated protein) was responsible for the elevated total m 6 A modification levels in EV71‐infected RD cells and that thioredoxin interacting protein (TXNIP) may be a target gene for demethylase FTO action. Further functional experiments showed that demethylase knockdown of FTO promoted TXNIP expression, activation of NLRP3 inflammasome and promoted the release of proinflammatory factors in vitro, and the opposite result occurred with demethylase FTO overexpression. And further tested in an animal model of EV71 infection in vitro, with results consistent with in vitro. Our findings elucidated that depletion of the demethylase FTO during EV71 infection increased the m 6 A modification level of TXNIP mRNA 3′ untranslated region (UTR), enhancing mRNA stability, and promoting TXNIP expression. Consequently, the NLRP3 inflammasome was stimulated, leading to the release of proinflammatory factors and facilitating HFMD progression.

We identified an individual who was coinfected with two SARS-CoV-2 variants of concern, the Beta and Delta variants. The ratio of the relative abundance between the two variants was maintained at 1:9 (Beta:Delta) in 14 days. Furthermore, possible evidence of recombinations in the Orf1ab and Spike genes was found.

BACKGROUND:Carvacrol is a monoterpenic phenol extracted from traditional Chinese herbs, including oregano and thyme. Currently, carvacrol has been widely studied for its therapeutic role in central nervous system diseases, liver diseases and digestive system cancer.OBJECTIVE:However, the role of carvacrol in osteosarcoma and its underlying molecular mechanism remain elusive. Here, we aimed to examine the anticancer effects of carvacrol on osteosarcoma.METHODS:The effects of carvacrol on the osteosarcoma proliferation capacity were revealed by CCK-8 and colony formation assays. Flow cytometry and Hoechst assays were used to determine the effects of carvacrol on osteosarcoma cell apoptosis. The effect of carvacrol on migration and invasion of osteosarcoma cells was determined by wound healing and transwell tests. Protein expression was evaluated by WB assays. The suppressive effects of carvacrol on osteosarcoma in vivo were examined by a xenograft animal model, immunohistochemistry and HE staining.RESULTS:We demonstrated that carvacrol treatment reduced viability and inhibited the colony formation of U2OS and 143B cells in a concentration-dependent manner. Apoptotic cell number increased after exposure to carvacrol. Meanwhile, the expression of Bax increased, and that of Bcl-2 decreased by carvacrol treatment. In addition, the MMP-9 expression and migration and invasion of 143B and U2OS cells were inhibited by carvacrol. We also found that these carvacrol-induced effects on osteosarcoma are associated with the regulation of the Wnt/β-catenin signaling pathway.CONCLUSION:Our findings suggest that carvacrol suppresses proliferation, migration, invasion and promotes apoptosis in osteosarcoma cells, in part by regulating the Wnt/β-catenin signaling pathway.

On January 13, 2022, Zhuhai CDC received a notification that a coronavirus disease 2019 (COVID-19) case was found in the fever clinic in nearby Zhongshan City. Zhuhai CDC promptly carried out large-scale population screening in three nearby counties. A total of 4 COVID-19 cases were found in Nanping county. 34 cases were screened from close contacts, and 2 cases were reported from close contacts in other cities of Guangdong Province. The 20 cases were sequenced by Guangdong CDC and identified as the variant of concern (VOC)/Omicron variant BA.1. Since January 14, Zhuhai has carried out 8 rounds of nucleic acid screening for COVID-19 in the county where the cases occurred. Four large-scale nucleic acid screening tests for COVID-19 were conducted across the city, and no new community cases were reported after January 15.

为了了解境外输入的新型冠状病毒(SARS-CoV-2)变异株的分子特征,本研究对2021年6月深圳市一株从南非输入的SARS-CoV-2毒株进行了全基因组测序和序列分析.Illumina测序技术获得的SARS-CoV-2毒株基因组长度为29567nt.根据"Pango lineages"分型法,本研究测定的毒株属于C.1.2系,该谱系属世界卫生组织定义的监测变异株(Variants Under Monitoring,VUM)成员之一.与参考株 Wuhan-Hu-1(NC_045512.2)比较,本研究 C.1.2系毒株共出现了 58个核苷酸变异位点,其中56个变异位点位于编码区.氨基酸变异位点共有33个,氨基酸变异位点分布于6个开放阅读框,变异数由多到少依次为:S蛋白区12个,ORFlab蛋白区9个,ORF3a蛋白区2个,M区2个,ORF8区2个,E区1个.本研究测定的SARS-CoV-2毒株属我国大陆首例境外输入的C.1.2变异株.开展境外输入的SARS-CoV-2毒株基于基因组测序的分子监测,对防控由境外输入的SARS-CoV-2变异株引起本地新型冠状病毒肺炎(COVID-19)暴发与流行具有重要意义.

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 The epidemiological investigation indicated that the patient (ACC-XG00731) began working as a security guard at the isolation point on July 25, 2020 in Shenzhen On January 19, his test result was negative According to his statement, in the last 14 days, he had worked on the isolation floor occasionally but had not been exposed to the individuals who were in quarantine, had no exposure to the household or medical waste generated from the isolation personnel, and did not participate in the sewage treatment of the isolation point On January 22, 2021, 1 case (ACC-XG00741) of COVID-19 infection in this isolation point was detected in entry isolation personnel from South Africa and was diagnosed on January 22 It was considered possible that case ACC-XG00731 is a descendant of the case ACC-XG00741 On January 25, 2021, the sample of the 2 cases were sequenced by Shenzhen CDC using the second-generation (MiSeq) and third-generation sequencing technology (Nanopore) Compared with the Wuhan reference (EPI_ISL_402125) (1), these 2 strains exhibited 23 to 24 nucleotide variation sites, belonging to the Pangolin lineage B 1 351 (2), which were all classified as the 20H/501 Y V2 variant (Figure 1) The genomic sequence of ACC-XG00731 and ACC-XG00741 strains were highly homologous (99 997%), sharing 23 variation sites (G174T, C241T, C1059T, A2692T, C3037T, G5230T, C9808T, A10323G, C14408T, C21614T, A21801C, A22206G, G22813T, A23403G, C23664T, G25477T, G25563T, C25904T, C26456T, C26645T, C28253T, C28887T, and G29737T) The 2021A-XG00731 strain only had one specific variation site (C16428T) As is characteristic of 501 Y V2 variant, the ACC-XG00731 strains carried several amino acid mutation sites, including K417N, E484K, and N501Y The 501Y V2 lineage, which was connected to a fast-growing epidemic, emerged in early August in South Africa (3) The 501Y V2 lineage includes several specific mutations (D80A, LAL242-244del, R246I, K417N, E484K, N501Y, D614G, and A701V) in the spike protein of the COVID-19 virus, also known as severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) The N501Y mutation had also been identified in the B 1 1 7 variant (also known as 501Y V1) first emerging in the United Kingdom (UK)(4);recently, the B 1 1 7 variant was estimated to be approximately 56% more transmissible than existing viruses in circulation (5) The N501Y mutation may influence the function of spike receptor binding domain (RBD) that promotes the interaction to ACE2 on the host cells, making infection easier (6) In the case that the 501Y V2 variant first emerging from South Africa was detected in returnees and further spread to the security guard at the isolation point in Shenzhen, the management measures of the isolation points should be heightened The 501Y V2 and 501Y V1 variant had been detected in Guangdong (7) and Shanghai in China, respectively (8), and had been identified in tens of countries worldwide, posing a more serious challenge to the global epidemic Understanding the faster-spreading variants of COVID-19 virus may be beneficial for the policy decisions to contain their spread

In-fight transmission of SARS-CoV-2 Delta variant could occur on airplane, and close contact is the main mode of transmission. Vaccination still protects against the Delta variant transmission.

Background Norovirus (NoV) is the main cause of non-bacterial acute gastroenteritis (AGE) outbreaks worldwide. From September 2015 through August 2018, 203 NoV outbreaks with 2,500 patients were reported to the Shenzhen Center for Disease Control and Prevention. Methods Fecal specimens were collected from the 203 outbreaks and epidemiological data were collected through the AGE outbreak surveillance system in Shenzhen. The genotypes were determined by sequencing analysis. To gain a better understanding of evolutionary characterization of NoV in Shenzhen, the molecular evolution was analyzed by time-scale evolutionary phylogeny and amino acid mutations. Results Most of these outbreaks were associated with NoV GII.P16/GII.2 strain (45.3%,92/203) and occurred in school settings (91.6%,186/203). The timescale phylogeny suggested that the GII.P16/GII.2 strain was recombination strain and were still stable. The amino acid mutations suggested that the nonstructural proteins of the recombination strain might play a more significant role than VP1 gene in these GII.P16/GII.2 recombination strain outbreaks. Conclusions This study illustrated the characteristics of the molecular epidemiological patterns in Shenzhen, China during September 2015 to August 2018 and provided the evidence that the GII.P16/GII.2 strain was static and the epidemic trend had fade.

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, oropharyngeal swab, and anal swab was sent to the virology laboratory of Shenzhen Center for Disease Control and Prevention (Shenzhen CDC) and was confirmed positive for SARS-CoV-2 by a qRT-PCR method simultaneously implemented in two commercial kits (Daan, Guangzhou, China and Bojie, Shanghai, China) (Supplementary Table S1, available in http://weekly.chinacdc.cn/).This patient tested negative for SARS-CoV-2 on June 8, 2021 and participated in an epidemiological investigation and sampling in a flight from South Africa that arrived at Baoan International Airport on June 10, 2021.Between June 10, 2021 and June 25, 2021, a total of 39 passengers (Case 1 to 39) from this flight were confirmed to be infected with SARS-CoV-2 in the virology laboratory of Shenzhen CDC.On June 17, 2021, a third-party laboratory detected SARS-CoV-2 in a mixed specimen of 10 swabs from ten individuals by qRT-PCR method, and the preliminary result was positive.This mixed specimen and one (Case B) of ten nasopharyngeal swabs from ten individuals were confirmed positive for SARS-CoV-2 in the virology laboratory of Shenzhen CDC.Case B was a 22-year-old female who worked in a restaurant at Baoan International Airport.The third case (Case C) lived in Dongguan City and worked in

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. On May 21, 2021, 3 types of specimens (nasopharyngeal swab, oropharyngeal swab, and anal swab) from this case were collected by Yantian CDC and were confirmed positive for COVID-19 virus by a RT-qPCR method simultaneously implemented in two commercial kits (Daan, Guangzhou, China and Bojie, Shanghai, China) in the virology laboratory of Shenzhen CDC (Table 1). Then, screening was initiated for employees from the Yantian Port and close contacts. A total of 5 cases were confirmed with COVID-19 infections between May 22, 2021 and May 24, 2021 (Table 1). These cases were transported immediately to the Shenzhen Third People’s Hospital for isolated treatment by ambulance after COVID-19 virus infection was confirmed. Specimens from the cases above collected by the Shenzhen Third People’s Hospital were sent to the virology laboratory of Shenzhen CDC for discharge assessment. High-throughput sequencing was performed for six COVID-19 virus strains from this study. First, viral RNA was extracted directly from 200-μL swab samples with the lowest Ct value in RT-qPCR tests using a High Pure Viral RNA Kit (Roche, Germany). Second, libraries were prepared using a Nextera® XT Library Prep Kit (Illumina, USA), and the resulting DNA libraries were sequenced on a MiSeq platform (Illumina) using a 300-cycle reagent kit (1). Last, mapped assemblies were generated using the COVID-19 virus/SARS-CoV-2 reference sequence Wuhan-Hu-1 (GenBank no. NC_045512.2). Nucleotide (nt) and amino acid (AA) differences between the six virus genome sequences from this study and the reference sequence Wuhan-Hu-1 were analyzed using the programs BioEdit 7.19 and MEGA version7 (2). The 6 strains from Case A, Case B, Case C, Case D, Case E, and Case F were designated as hCoV-19/Guangdong/IVDC-05-01-2/2021, hCoV-19/Guangdong/IVDC-05-02-2/2021, hCoV-19/Guangdong/IVDC-05-03/2021, hCoV-19/Guangdong/IVDC-05-04/2021, hCoV19/Guangdong/IVDC-05-05/2021, and hCoV-19/Guangdong/IVDC-05-06/2021, respectively, in this study. The genome sequences of these 6 strains were 29,844 nt, 29,867nt, 29,808 nt, 29,846 nt, 29,760 nt, and 29,832nt in length, respectively. Based on the “Pango lineages” rule (3), the 6 virus strains from this study were assigned to lineage B.1.1.7, which was also known as Variant of Concern 202012/01 (VOC-202012/01) or 20B/501Y.V1. The lineage B.1.1.7 was first identified in the UK in September 2020 and had 24 characteristic mutations (ORF1a: T1001I, A1708D, I2230T, del3675-3677;ORF1b: P314L;S: del69/70, del144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H;ORF8:Q27stop, R52I, Y73C;N: D3L, R203K, G204R, S235F). Compared with the reference genome sequence Wuhan-Hu-1, 5 strains (hCoV-19/Guangdong/IVDC-05-01-2/2021, hCoV-19/Guangdong/IVDC-05-02-2/2021, hCoV-19/Guangdong/IVDC-05-03/2021, hCoV-19/Guangdong/IVDC-05-04/2021, and hCoV-19/Guangdong/IVDC-05-06/2021) displayed 38 nucleotide variation sites (C241T, C643T, C913T, C2536T, A2784G, C3037T, C3267T, C5388A, C5986T, T6954C, C7851T, G13975T, C14408T, C14676T, T15096C, C15279T, T16176C, C17430T, G17944T, G21578T, A23063T, C23271A, A23403G, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28111G, G28280C, A28281T, T28282A, G28739T, G28881A, G28882A, G28883C, and C28977T) and 18 deletion mutations (ORF1a: del11288-11296/TCTGGTTTT;S: del21766-21771/ACATGT, del21994-21996/TTA). Except for the mutations above, other two variation sites (ORF1a: C884T and S: A23898T) were observed in genome of the strain hCoV-19/Guangdong/IVDC-05-05/2021 (Case E). By comparing deduced amino acid sequences, the 5 SARS-CoV-2 strains (hCoV-19/Guangdong/IVDC-05-01-2/2021, hCoV-19/Guangdong/IVDC-05-02-2/2021, hCoV-19/Guangdong/IVDC-05-03/2021, hCoV-19/Guangdong/IVDC-05-04/2021, and hCoV-19/Guangdong/IVDC-05-06/2021) displayed 24 AA variation sites (ORF1a: N840S, T1001I, A1708D, I2230T, A2529V;ORF1b: G170C, P314L, V1493L;S: V6F, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H;ORF8: Q27stop, R52I, Y73C;N: D3L, A156S, R203K, G204R, and S235F) and 6 deletion mutations (ORF1a: S3675del, G3675del, and F3677 del;S: H69del, V70del, and Y144del). Except for the mutations above, 2 other variation sites (ORF1a: R207C;S: Q779L) were observed in amino acid sequence of the strain hCoV-19/Guangdong/IVDC-05-05/2021 (Case E). All of the characteristic mutations belonging to SARS-CoV-2 variant B.1.1.7 were found in genomes of the 6 SARS-CoV-2 strains from this study. Whole-genome sequencing (WGS) confirmed that all SARS-CoV-2 strains from this study were VOC 202012/01-lineage B.1.1.7, suggesting a common source of exposure at the Yantian Port. SARS-CoV-2 lineage B.1.1.7 is of growing concern because it has shown to be significantly more transmissible than other variants (4-7). As of now, the 4 SARS-CoV-2 VOCs (B.1.1.7, B.1.351, P.1, and B.1.617.2) have been imported into mainland China (8-11). There is a high risk that imported SARS-CoV-2 VOCs may cause local outbreaks and epidemics. In this study, we focused on laboratory testing and genome characterization of the pathogen. Detailed epidemiological investigation is essential in a follow-up report. Data availability: The six SARS-CoV-2 genome sequences determined in this study has been deposited in GISAID (www.gisaid.org) under the accession number EPI_ISL_2405168, EPI_ISL_2405169, EPI_ISL_2432955, EPI_ISL_2405170, EPI_ISL_2405171, and EPI_ISL_2405172.