Symptomatic COVID-19 in University Students: A School-Wide Web-Based Questionnaire Survey during the Omicron Variant Outbreak

Aim: To detect risk and preventive factors associated with the Omicron variant infection in university students, a combination of a web-based survey and multivariate logistic regression analysis was introduced as the front-line initiatives by the school health practitioners. Design: Questionnaire survey. Methods: The school-wide web-based questionnaire survey was conducted among our university students as a part of the annual health check-up in April, 2023. The positive outcome was confined to the first symptomatic COVID-19 onset during the Omicron variant outbreak. Results: In this self-administered survey, risk or protective associations were merely estimated statistically in university students (n = 5406). In measured factors, karaoke and club/group activities could maintain the statistical significance in adjusted odds ratios (ORs) as relative risk factors, and science course, measles/ rubella (MR) vaccination, and COVID-19 vaccination remained as relative protective factors in adjusted OR analyses. Club/group activities with member gathering and karaoke sing-along sessions in university students may frequently have WHO’s three Cs. These risk factors are still important topics for the infection control of COVID-19 in university students. Together with some recent reports from other researchers, the significant protective role of MR vaccine in our survey warrants further clinical investigation. If the breakthrough infection continuously constitutes the majority of infection, real data in test-negative case-control or web-based questionnaire design continue to be important for statistical analysis to determine the minimal requirement of our strategies which may be equivalent to or replace COVID-19 vaccines.

Chest computed tomography findings of the Omicron variants of SARS-CoV-2 with different cycle threshold values

BACKGROUND The Omicron variant of severe acute respiratory syndrome coronavirus 2(SARSCoV-2)mainly infects the upper respiratory tract.This study aimed to determine whether the probability of pulmonary infection and the cycle threshold(Ct)measured using the fluorescent polymerase chain reaction(PCR)method were related to pulmonary infections diagnosed via computed tomography(CT).AIM To analyze the chest CT signs of SARS-CoV-2 Omicron variant infections with different Ct values,as determined via PCR.METHODS The chest CT images and PCR Ct values of 331 patients with SARS-CoV-2Omicron variant infections were retrospectively collected and categorized into low(<25),medium(25.00-34.99),and high(≥35)Ct groups.The characteristics of chest CT images in each group were statistically analyzed.RESULTS The PCR Ct values ranged from 13.36 to 39.81,with 99 patients in the low,155 in the medium,and 77 in the high Ct groups.Six abnormal chest CT signs were detected,namely,focal infection,patchy consolidation shadows,patchy groundglass shadows,mixed consolidation ground-glass shadows,subpleural interstitial changes,and pleural changes.Focal infections were less frequent in the low Ct group than in the medium and high Ct groups;these infections were the most common sign in the medium and high Ct groups.Patchy consolidation shadows and pleural changes were more frequent in the low Ct group than in the other two groups.The number of patients with two or more signs was greater in the low Ct group than in the medium and high Ct groups.CONCLUSION The chest CT signs of patients with pulmonary infection caused by the Omicron variants of SARSCoV-2 varied depending on the Ct values.Identification of the characteristics of Omicron variant infection can help subsequent planning of clinical treatment.

Omicron variant (B.1.1.529) of SARS-CoV-2: Mutation, infectivity, transmission, and vaccine resistance

The appearance of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variant Omicron(B.1.1.529)has caused panic responses around the world because of its high transmission rate and number of mutations.This review summarizes the highly mutated regions,the essential infectivity,transmission,vaccine breakthrough and antibody resistance of the Omicron variant of SARSCoV-2.The Omicron is highly transmissible and is spreading faster than any previous variant,but may cause less severe symptoms than previous variants.The Omicron is able to escape the immune system’s defenses and coronavirus disease 2019 vaccines are less effective against the Omicron variant.Early careful preventive steps including vaccination will always be key for the suppression of the Omicron variant.

Efficacyand Safetyof Huashi Baidu Granules in Treating Patients with SARS-CoV-2Omicron Variant: A Single-Center Retrospective Cohort Study

Objective:To evaluate the efficacy and safety of Huashi Baidu Granules(HSBD)in treating patients with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)Omicron variant.Methods:A single-center retrospective cohort study was conducted during COVID-19 Omicron epidemic in the Mobile Cabin Hospital of Shanghai New International Expo Center from April 1st to May 23rd,2022.All COVID-19 patients with asymptomatic or mild infection were assigned to the treatment group(HSBD users)and the control group(non-HSBD users).After propensity score matching in a 1:1 ratio,496 HSBD users of treatment group were matched by propensity score to 496 non-HSBD users.Patients in the treatment group were administrated HSBD(5 g/bag)orally for 1 bag twice a day for 7 consecutive days.Patients in the control group received standard care and routine treatment.The primary outcomes were the negative conversion time of nucleic acid and negative conversion rate at day 7.Secondary outcomes included the hospitalized days,the time of the first nucleic acid negative conversion,and new-onset symptoms in asymptomatic patients.Adverse events(AEs)that occurred during the study were recorded.Further subgroup analysis was conducted in vaccinated(378 HSBD users and 390 non-HSBD users)and unvaccinated patients(118 HSBD users and 106 non-HSBD users).Results:The median negative conversion time of nucleic acid in the treatment group was significantly shortened than the control group[3 days(IQR:2-5 days)vs.5 days(IQR:4-6 days);P<0.01].The negative conversion rate of nucleic acid in the treatment group were significantly higher than those in the control group at day 7(91.73%vs.86.90%,P=0.014).Compared with the control group,the hospitalized days in the treatment group were significantly reduced[10 days(IQR:8-11 days)vs.11 days(IQR:10.25-12 days);P<0.01].The time of the first nucleic acid negative conversion had significant differences between the treatment and control groups[3 days(IQR:2-4 days)vs.5 days(IQR:4-6 days);P<0.01].The incidence of new-onset symptoms including cough,pharyngalgia,expectoration and fever in the treatment group were lower than the control group(P<0.05 or P<0.01).In the vaccinated patients,the median negative conversion time and hospitalized days were significantly shorter than the control group after HSDB treatment[3days(IQR:2-5days)vs.5 days(IQR:4-6 days),P<0.01;10 days(IQR:8-11 days)vs.11 days(IQR:10-12 days),P<0.01].In the unvaccinatedpatients,HSBD treatment efficiently shorten the median negative conversion time and hospitalized days[4 days(IQR:2-6 days)vs.5 days(IQR:4-7 days),P<0.01;10.5 days(IQR:8.75-11 days)vs.11.0 days(IQR:10.75-13 days);P<0.01].No serious AEs were reported during the study.Conclusion:HSBD treatment significantly shortened the negative conversion time of nuclear acid,the length of hospitalization,and the time of the first nucleic acid negative conversion in patients infectedwith SARS-COV-2Omicronvariant(Trial registry No.ChiCTR2200060472).

A human monoclonal antibody neutralizes SARS-CoV-2 Omicron variants bytargeting the upstream region of spike protein HR2 motif

The continuous emergence of new severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variants meansthere is a need to explore additional strategies to develop broad-spectrum vaccines or therapeutics for individuals remaining at risk of coronavirus disease 2019(COVID-19).Neutralizing monoclonal antibody(mAb)that binds to theconserved S2 subunit of the SARS-CoV-2 spike(S)protein alone,or in combination with mAb that binds to the receptor-binding domain(RBD)of S protein,might be effective in eliciting protection from infection by a variety of SARS-CoV2 variants.Using high-throughput single-cell immunoglobulin sequencing of B cells from COVID-19-convalescent donors,we identified a high-affinity S2-specific mAb-39,that could inhibit original SARS-CoV-2 strain,Omicron BA.1,BA.2.86,BA.4,BA.5,and EG.5.1 S protein-mediated membrane fusion,leading to the neutralization of these pseudoviralinfections.Moreover,mAb-39 could also improve the neutralizing activity of anti-RBD antibody against the highlyneutralization-resistant Omicron variants.Molecular docking and point mutation analyses revealed that mAb-39 recognized epitopes within the conserved upstream region of the heptad repeat 2(HR2)motif of the S2 subunit.Collectively,these findings demonstrate that targeting the conserved upstream region of the HR2 motif(e.g.,using mAbs)provides anovel strategy for preventing the infection of SARS-CoV-2 and its variants.

Clinical characteristics of pediatric cases infected with the SARS-CoV-2 Omicron variant in a tertiary children's medical center in Shanghai,China

Background The number of pediatric cases of infection with the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)Omicron variant has increased.Here,we describe the clinical characteristics of children in a tertiary children's medical center in Shanghai.Methods A total of 676 pediatric coronavirus disease 2019(COVID-19)cases caused by the Omicron variant who were admitted to the Shanghai Children's Medical Center from March 28 to April 30,2022 were enrolled in this single-center,prospective,observational real-world study.Patient demographics and clinical characteristics,especially COVID-19 vaccine status,were assessed.Results Children of all ages appeared susceptible to the SARS-CoV-2 Omicron variant,with no significant difference between sexes.A high SARS-CoV-2 viral load upon admission was associated with leukocytopenia,neutropenia,and thrombocytopenia(P=0.003,P=0.021,and P=0.017,respectively)but not with physical symptoms or radiographic chest abnormalities.Univariable linear regression models indicated that comorbidities(P=0.001)were associated with a longer time until viral clearance,and increasing age(P<0.001)and two doses of COVID-19 vaccine(P=0.001)were associated with a shorter time to viral clearance.Multivariable analysis revealed an independent effect of comorbidities(P<0.001)and age(P=0.003).The interaction effect between age and comorbidity showed that the negative association between age and time to virus clearance remained significant only in patients without underlying diseases(P<0.001).Conclusion This study describes the clinical characteristics of children infected with the Omicron variant of SARS-CoV-2 and calls for additional studies to evaluate the effectiveness and safety of vaccination against COVID-19 in children.

Mathematical modeling for Delta and Omicron variant of SARS-CoV-2 transmission dynamics in Greece

A compartmental,epidemiological,mathematical model was developed in order to analyze the transmission dynamics of Delta and Omicron variant,of SARS-CoV-2,in Greece.The model was parameterized twice during the 4th and 5th wave of the pandemic.The 4th wave refers to the period during which the Delta variant was dominant(approximately July to December of 2021)and the 5th wave to the period during which the Omicron variant was dominant(approximately January to May of 2022),in accordance with the official data from the National Public Health Organization(NPHO).Fitting methods were applied to evaluate important parameters in connection with the transmission of the variants,as well as the social behavior of population during these periods of interest.Mathematical models revealed higher numbers of contagiousness and cases of asymptomatic disease during the Omicron variant period,but a decreased rate of hospitalization compared to the Delta period.Also,parameters related to the behavior of the population in Greece were also assessed.More specifically,the use of protective masks and the abidance of social distancing measures.Simulations revealed that over 5,000 deaths could have been avoided,if mask usage and social distancing were 20%more efficient,during the short period of the Delta and Omicron outbreak.Furthermore,the spread of the variants was assessed using viral load data.The data were recorded from PCR tests at 417 Army Equity Fund Hospital(NIMTS),in Athens and the Ct values from 746 patients with COVID-19 were processed,to explain transmission phenomena and disease severity in patients.The period when the Delta variant prevailed in the country,the average Ct value was calculated as 25.19(range:12.32e39.29),whereas during the period when the Omicron variant prevailed,the average Ct value was calculated as 28(range:14.41e39.36).In conclusion,our experimental study showed that the higher viral load,which is related to the Delta variant,may interpret the severity of the disease.However,no correlation was confirmed regarding contagiousness phenomena.The results of the model,Ct analysis and official data from NPHO are consistent.

Omicron variants breakthrough infection elicited higher specific memory immunity than third dose booster in healthy vaccinees

Homologous booster,heterologous booster,and Omicron variants breakthrough infection(OBI)could improve the humoral immunity against Omicron variants.Questions concerning about memory B cells(MBCs)and T cells immunity against Omicron variants,features of long-term immunity,after booster and OBI,needs to be explored.Here,comparative analysis demonstrate antibody and T cell immunity against ancestral strain,Delta and Omicron variants in Omicron breakthrough infected patients(OBIPs)are comparable to that in Ad5-nCoV boosted healthy volunteers(HVs),higher than that in inactivated vaccine(InV)boosted HVs.However,memory B cells(MBCs)immunity against Omicron variants was highest in OBIPs,followed by Ad5-nCoV boosted and InV boosted HVs.OBIPs and Ad5-nCoV boosted HVs have higher classical MBCs and activated MBCs,and lower naïve MBCs and atypical MBCs relative to both vaccine boosted HVs.Collectively,these data indicate Omicron breakthrough infection elicit higher MBCs and T cells against SARS-CoV-2 especially Omicron variants relative to homologous InV booster and heterologous Ad5-nCoV booster.

上海市某方舱医院2897例新型冠状病毒Omicron变异株轻型/无症状感染者住院时间影响因素分析

目的探讨上海市某方舱医院新型冠状病毒奥密克戎(Omicron)变异株轻型/无症状感染者住院时间的影响因素。方法回顾性收集上海宝山泾灿路(罗泾京东)方舱医院收治的2897例Omicron变异株轻型/无症状感染者的病历资料,分析其一般资料、住院时间等基本情况,探究不同特征的新冠病毒Omicron变异株感染者住院时间差异,采用多重线性回归方法分析住院时间的影响因素。根据单因素分析结果,采用二元logistic回归分析住院时间≥14 d可能的影响因素。结果2897例Omicron变异株轻型/无症状感染者的平均住院时间为(9.1±4.6)d,不同年龄段、入舱前核酸阳性时间以及伴有咳嗽、咳痰、咽痛、发热、流涕、鼻塞、口干咽燥、头痛、乏力、肌痛、腹泻、恶寒、恶心呕吐、头晕症状的感染者住院时间不同,差异具有统计学意义(P<0.05)。多重线性回归结果显示,年龄增加、患有糖尿病史以及咽痛、发热、流涕、肌痛症状会增加住院天数,而入舱前核酸阳性时间长则会减少住院天数。住院时间≥14 d者,高龄、糖尿病史以及出现咽痛、发热、口干咽燥、肌痛、恶心呕吐症状的占比更高,入舱前核酸阳性时间相对更短,接种2针及以上疫苗占比更低,差异具有统计学意义(P<0.05)。二元Logistic回归结果显示,高龄、入舱前核酸阳性时间短、糖尿病史以及发热和口干咽燥症状可能是导致住院时间超过14 d的危险因素,接种2针及以上疫苗可能是保护因素。结论Omicron变异株轻型/无症状感染者平均住院时间约为9 d,高龄、疫苗接种2针及以上、患有糖尿病史、入舱前核酸阳性时间短以及咽痛、发热、流涕、口干咽燥、肌痛等正气虚衰、病邪入里、化热伤阴表现对于住院时间可能产生重要影响。通过尽早识别核酸转阴慢、住院时间长的高危患者,以期为缩短核酸转阴时间、指导重点人群精准防控提供指导方向。

SARS-CoV-2 Omicron变异株多重微滴式数字PCR定量方法的建立及应用

【目的】为建立精准、高效的多重微滴式数字PCR(droplet digital PCR,ddPCR)定量分析检测方法,开发可同时鉴别新型冠状病毒(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)ORF1ab基因、N基因、E基因以及Omicron变异株S基因的检测体系,提高病毒性传染疾病的诊断效率及传播风险监测能力。【方法】通过筛选保守基因序列并设计特异性引物与探针,优化反应体系和扩增程序,对该方法的特异性、灵敏度及稳定性进行评价。以临床样本为实验材料,利用建立的ddPCR方法进行检测和验证,确定阳性检出率。【结果】多重ddPCR反应体系中,各对引物探针对目的片段均能有效扩增,SARS-CoV-2 ORF1ab基因、N基因、E基因以及Omicron变异株S基因灵敏度检测下限分别为0.59、0.68、1.44、1.03 copies/μL。在20份临床样本的核酸检测中,共检出16份阳性样本,阳性率达80%(16/20),经荧光定量PCR方法复测符合率一致。【结论】研究建立的多重ddPCR方法特异性强、灵敏度高,可实现对临床样本中微量新冠病毒的精确定量检测。

新型冠状病毒Omicron I1566V突变位点MS2噬菌体病毒样颗粒的构建

目的构建新型冠状病毒Omicron I1566V突变位点MS2噬菌体病毒样颗粒。方法选取并合成带有6×His标签的MS2噬菌体的衣壳蛋白(CP)、成熟蛋白(A蛋白)及Omicron I1566V突变基因序列,插入pACYCDuet-1质粒构建重组载体,通过原核系统诱导表达目的蛋白,纯化重组蛋白后利用透射电镜对蛋白质进行物理表征,最后通过反转录聚合酶链反应(RT-PCR)检测病毒样颗粒的热稳定性及耐核酸酶水解能力。结果成功构建包含有6×His标签的CP、A蛋白和Omicron I1566V突变基因序列的重组载体,经限制性内切酶BamHⅠ和KpnⅠ酶切鉴定和测序验证,结果均与预期相符。经诱导并纯化后,通过电镜观察到了大小均匀、直径为23~28 nm的病毒样颗粒,该病毒样颗粒经核酸酶消化后可在37℃条件下稳定储存20 d以上。结论该研究成功利用MS2噬菌体的CP和A蛋白构建了Omicron I1566V突变位点病毒样颗粒,为该突变位点的RT-PCR检测体系提供了可靠的质量保障。

Nasal delivery of broadly neutralizing antibodies protects mice from lethal challenge with SARS-CoV-2 delta and omicron variants

Multiple new variants of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)have constantly emerged,as the delta and omicron variants,which have developed resistance to currently gained neutralizing antibodies.This highlights a critical need to discover new therapeutic agents to overcome the variants mutations.Despite the availability of vaccines against coronavirus disease 2019(COVID-19),the use of broadly neutralizing antibodies has been considered as an alternative way for the prevention or treatment of SARS-Co V-2 variants infection.Here,we show that the nasal delivery of two previously characterized broadly neutralizing antibodies(F61 and H121)protected K18-h ACE2 mice against lethal challenge with SARS-Co V-2 variants.The broadly protective efficacy of the F61 or F61/F121 cocktail antibodies was evaluated by lethal challenge with the wild strain(WIV04)and multiple variants,including beta(B.1.351),delta(B.1.617.2),and omicron(B.1.1.529)at 200or 1000 TCID_(50),and the minimum antibody administration doses(5-1.25 mg/kg body weight)were also evaluated with delta and omicron challenge.Fully prophylactic protections were found in all challenged groups with both F61 and F61/H121 combination at the administration dose of 20 mg/kg body weight,and corresponding mice lung viral RNA showed negative,with almost all alveolar septa and cavities remaining normal.Furthermore,low-dose antibody treatment induced significant prophylactic protection against lethal challenge with delta and omicron variants,whereas the F61/H121 combination showed excellent results against omicron infection.Our findings indicated the potential use of broadly neutralizing monoclonal antibodies as prophylactic and therapeutic agent for protection of current emerged SARS-Co V-2 variants infection.

Importation of SARS-CoV-2 Omicron variant in Beijing,China

Omicron(B.1.1.529),the fifth variant of concern(VOC)of severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2),was firstly identified in November 2021 in South Africa.Omicron contains far more genome mutations than any other VOCs ever found,raising significant concerns about its increased transmissibility and immune evasion.Here,we report the importation of the Omicron variant into Beijing,China,in December 2021.Full‐length genome sequences of five imported strains were obtained,with their genetic features characterized.Each strain contained 57 to 61 nucleotide substitutions,39 deletions,and 9 insertions in the genome.Thirty to thirty‐two amino acid changes were found in the spike proteins of the five strains.The phylogenetic tree constructed by the maximum likelihood method showed that all five imported genomes belonged to Omicron(BA.1)(alias of B.1.1.529.1),which is leading to the current surge of coronavirus disease 2019(COVID‐19)cases worldwide.The globally increased COVID‐19 cases driven by the Omicron variant pose a significant challenge to disease prevention and control in China.Continuous viral genetic surveillance and increased testing among international travellers are required to contain this highly contagious variant.

Clinical and immunological features of convalescent pediatric patients infected with the SARS-CoV-2 Omicron variant in Tianjin, China

COVID-19 has spread surprisingly fast worldwide, and new variants continue to emerge. Recently, the World Health Organization acknowledged a new mutant strain “Omicron”, with children were accounting for a growing share of COVID-19 cases compared with other mutant strains. However, the clinical and immunological characteristics of convalescent pediatric patients after Omicron infection were lacking. In this study, we comparatively analyzed the clinical data from pediatric patients with adult patients or healthy children and the effects of SARSCoV-2 vaccine on the clinical and immune characteristics in convalescent pediatric patients. Our results indicated that convalescent pediatric patients had unique clinical and immune characteristics different from those of adult patients or healthy children, and SARS-CoV-2 vaccination significantly affected on the clinical and immune characteristics and the prevention of nucleic acid re-detectable positive(RP) in convalescent patients. Our study further deepens the understanding of the impact of Omicron on the long-term health of pediatric patients and provides a valuable reference for the prevention and treatment of children infected with Omicron.

Omicron变异株感染导致儿童热性惊厥的临床特征分析

目的分析儿童感染Omicron变异株后发生热性惊厥的临床特征。方法回顾性收集2022年12月1—31日(Omicron变异株流行期间,设为Omicron组)和2021年同期(非Omicron组)就诊于首都儿科研究所附属儿童医院神经内科热性惊厥患儿的临床资料,分析比较两组患儿的临床特征。结果Omicron组381例,男性250例,女性131例,平均年龄(3.2±2.4)岁。非Omicron组112例,男性72例,女性40例,平均年龄(3.5±1.8)岁。Omicron组人数明显增多,是非Omicron组的3.4倍。Omicron组1岁~和6~10.83岁两个年龄段患儿占比高于非Omicron组,4岁~和5岁~两个年龄段患儿占比低于非Omicron组(P<0.05)。Omicron组丛集性发作和惊厥持续状态比例高于非Omicron组(P<0.05)。热性惊厥复发患儿中,Omicron组6~10.83岁占比高于非Omicron组,3岁~、4岁~、5岁~占比低于非Omicron组(P<0.05)。结论儿童感染Omicron变异株后热性惊厥的特征是年龄范围更广,在一次发热病程中丛集性发作和惊厥持续状态的比例增加。

Origin and evolutionary analysis of the SARS-CoV-2 Omicron variant

The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has evolved rapidly into new variants throughout the pandemic.The Omicron variant has more than 50 mutations when compared with the original wild-type strain and has been identified globally in numerous countries.In this report,we analyzed the mutational profiles of several variants,including the per-site mutation rate,to determine evolutionary relationships.The Omicron variant was found to have a unique mutation profile when compared with that of other SARS-CoV-2 variants,containing mutations that are rare in clinical samples.Moreover,the presence of five mouse-adapted mutation sites suggests that Omicron may have evolved in a mouse host.Mutations in the Omicron receptor-binding domain(RBD)region,in particular,have potential implications for the ongoing pandemic.

Clinical practice of rapid antigen tests for SARS-CoV-2 Omicron variant:A single-center study in China

Responding to the fast-spreading SARS-CoV-2 Omicron variant, to improve screening efficiency, rapid antigen tests(RATs) were first added as a supplementary detection method in China in mid-March, 2022. What and how big a role RATs should play need to be supported by clinical data. Here, RAT performance and relevant factors in comparison with nucleic acid amplification tests(NAATs) were assessed in Omicron-infected inpatients. From the NAAT results, nasopharyngeal swabs(NPs) performed better than oropharyngeal swabs(OPs). RATs tested on NAAT positive NPs performed better than those with OP-positive samples. The RAT positivity rate was strongly associated with high levels of N and OFR1ab genes, especially in NPs where patients also had significantly longer hospital stays and shorter days from symptom onset to RAT testing. Self-performed RATs had a detection accuracy that was comparable to professionally performed RATs when the subjects were well guided. The antigen negative rate of the studied patients was 100% at discharge. These findings suggest that, in addition to a supplementary detection role, RATs can be an important strategy for evaluating the disease progression of Omicron-infected inpatients. This study provides important clinical data to support better rules regarding RATs under China’s COVID-19 prevention and control policy.

Sanger Sequencing for Molecular Diagnosis of SARS-CoV-2 Omicron Subvariants and Its Challenges

Large population passages of the SARS-CoV-2 in the past two and a half years have allowed the circulating virus to accumulate an increasing number of mutations in its genome. The most recently emerging Omicron subvariants have the highest number of mutations in the Spike (S) protein gene and these mutations mainly occur in the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the S gene. The European Centre for Disease Prevention and Control (eCDC) and the World Health Organization (WHO) recommend partial Sanger sequencing of the SARS-CoV-2 S gene RBD and NTD on the polymerase chain reaction (PCR)-positive samples in diagnostic laboratories as a practical means of determining the variants of concern to monitor possible increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them. The author’s diagnostic laboratory has implemented the eCDC/WHO recommendation by sequencing a 398-base segment of the N gene for the definitive detection of SARS-CoV-2 in clinical samples, and sequencing a 445-base segment of the RBD and a 490 - 509-base segment of the NTD for variant determination. This paper presents 5 selective cases to illustrate the challenges of using Sanger sequencing to diagnose Omicron subvariants when the samples harbor a high level of co-existing minor subvariant sequences with multi-allelic single nucleotide polymorphisms (SNPs) or possible recombinant Omicron subvariants containing a BA.2 RBD and an atypical BA.1 NTD, which can only be detected by using specially designed PCR primers. In addition, Sanger sequencing may reveal unclassified subvariants, such as BA.4/BA.5 with L84I mutation in the S gene NTD. The current large-scale surveillance programs using next-generation sequencing (NGS) do not face similar problems because NGS focuses on deriving consensus sequence.

The latest research progress of novel coronavirus "Omicron sub-variant BA.5"

Since the outbreak of COVID-19,severe acute respiratory syndrome coronavirus 2 genome is still mutating,forming a variety of variants with strong transmission capacity,causing the spread of the epidemic worldwide,posing a serious threat to people's physical and mental health,and posing a major challenge to global public health.Omicron remains the main variant in several outbreaks worldwide,accounting for about 99%of the global genetic sequence.Recently,the World Health Organization announced that the subvariant of Omicron BA.5 has been found in more than 100 countries and regions around the world,causing the global epidemic rebound.However,there are few studies on the subvariant BA.5.This article reviews the latest research progress in epidemiology,infectivity,pathogenicity,vaccine and monoclonal antibody protection against Omicron subvariant BA.5,in order to provide reference for scientific prevention and control of Omicron subvariant BA.5.

24例新生儿新型冠状病毒Omicron变异株感染的临床特征分析

目的 分析新生儿新型冠状病毒Omicron变异株感染病例的临床特点。方法 收集新型冠状病毒Omicron变异株感染新生儿24例为感染组,非感染组29例为对照组。分析感染患儿的临床特征及转归,比较两组患儿的炎症指标和其他实验室指标水平。结果 感染患儿在生后均有新型冠状病毒感染阳性家庭成员密切接触史。临床分型均为轻型,21例(87.50%)患儿出现发热,多伴有1种或几种其他症状。感染组结果显示4例(16.67%)白细胞计数降低,8例(33.33%)淋巴细胞计数降低;2例(9.52%)天冬氨酸氨基转移酶升高,21例(100%)前白蛋白均降低;5例(26.32%)胱抑素C升高;1例(4.76%)肌酸激酶升高,19例(90.48%)乳酸脱氢酶升高。与对照组比较,感染组血白细胞、淋巴细胞、淋巴细胞/单核细胞比值(LMR)、前白蛋白水平均显著降低(P<0.01﹚,血小板/淋巴细胞比值(PLR)、天冬氨酸氨基转移酶、胱抑素C、肌酸激酶、乳酸脱氢酶水平均显著升高(P<0.05﹚。所有患儿对症治疗后均痊愈出院,住院时间中位数为5d。结论Omicron变异株感染新生儿病例表现为轻型,临床症状主要为发热,病程呈自限性。感染患儿多伴有淋巴细胞计数降低,肌酸激酶、乳酸脱氢酶水平升高,LMR、PLR异常及低前白蛋白水平对于新型冠状病毒(COVID-19)感染的早期诊断具有重要的临床价值。