PCR-HRM for Genomic Surveillance of SARS-CoV-2: A Variant Detection Tool in Côte d’Ivoire, West Africa

The rise of new viruses, like SARS-CoV-2 causing the COVID-19 outbreak, along with the return of antibiotic resistance in harmful bacteria, demands a swift and efficient reaction to safeguard the health and welfare of the global population. It is crucial to have effective measures for prevention, intervention, and monitoring in place to address these evolving and recurring risks, ensuring public health and international security. In countries with limited resources, utilizing recombinant mutation plasmid technology in conjunction with PCR-HRM could help differentiate the existence of novel variants. cDNA synthesis was carried out on 8 nasopharyngeal samples following viral RNA extraction. The P1 segment of the SARS-CoV-2 Spike S protein was amplified via conventional PCR. Subsequently, PCR products were ligated with the pGEM-T Easy vector to generate eight recombinant SARS-CoV-2 plasmids. Clones containing mutations were sequenced using Sanger sequencing and analyzed through PCR-HRM. The P1 segment of the S gene from SARS-CoV-2 was successfully amplified, resulting in 8 recombinant plasmids generated from the 231 bp fragment. PCR-HRM analysis of these recombinant plasmids differentiated three variations within the SARS-CoV-2 plasmid population, each displaying distinct melting temperatures. Sanger sequencing identified mutations A112C, G113T, A114G, G214T, and G216C on the P1 segment, validating the PCR-HRM findings of the variations. These mutations led to the detection of L452R or L452M and F486V protein mutations within the protein sequence of the Omicron variant of SARS-CoV-2. In summary, PCR-HRM is a vital and affordable tool for distinguishing SARS-CoV-2 variants utilizing recombinant plasmids as controls.

Contribution of Genomic Surveillance in the Detection and Monitoring of SARS-CoV-2 Variants during the 6 Pandemic Waves in the Central African Republic from 2020 to 2023

Objective: The COVID-19 pandemic has highlighted the need to strengthen diagnosis and genomic surveillance capacities. In 2021, Central African managed five waves of COVID-19 by integrating genomic surveillance into their health monitoring system. This study sought to report surveillance data from the National Laboratory of Clinical Biology and Public Health and describe the circulation of SARS-CoV-2 variants. Materials and Methods: This retrospective, descriptive observational study spans three years, from April 2020 to November 2023. It was conducted on a population of consenting volunteers from across the Central African Republic, who were tested using RT-PCR on nasopharyngeal samples. Data with sufficient information were obtained from the National Laboratory of Clinical Biology and Public Health (LNBCSP) databases. Sequencing was largely carried out at the National Institute of Biomedical Research (INRB) in Kinshasa until May 2023, and subsequently at the LNBCSP. Results and Discussion: Out of 97,864 RT-PCR tests performed, 9,764 were positive, resulting in a prevalence of 9.98%. The average age of the patients was 39.97 years ± 13.76, and the male-to-female sex ratio was 2.12. RT-PCR test positivity was significantly associated with age (p = 0.001), sex (p = 0.013) and clinical manifestations. Ten variants circulated during the five recorded waves, with Omicron (B.1.1.529), Delta (B.1.617.2) variants being predominant. Notably, the B.1.620 and B.640 variants were prominent during the second wave. Conclusion: This retrospective study provides key insights into the COVID-19 pandemic in the CAR. It identifies risk factors and details the circulation of various SARS-CoV-2 variants. Enhancing national genomic surveillance capacities would enable the country to better respond to future pandemic challenges.

SARS-CoV-2 Delta变异株:从结构变异到强传染力

严重急性呼吸综合征冠状病毒2(SARS-CoV-2)变体Delta变异株(B.1.617.2毒株),以极强的传播力迅速成为了目前世界范围的2019冠状病毒病(COVID-19)主要致病毒株。刺突蛋白作为冠状病毒的关键结构蛋白质,介导了SARS-CoV-2与靶细胞识别、结合及融合过程,与Delta变异株的高传染性密切相关。Delta变异株中刺突蛋白基因突变位点从其空间构象、表面亲水性与自由能等方面加以改变,影响了刺突蛋白与靶细胞膜的识别与融合过程,加速了结合进程。Delta变异株的分子结构及其功能研究对于COVID-19的预防及治疗至关重要。本文简述了SARS-CoV-2 Delta变异株相较于野生株的分子结构特点,着重以冠状病毒刺突蛋白为基础,回顾了中和抗体与血清之于Delta变异株的效力改变,并总结了SARS-CoV-2 Delta变异株的病毒动力学及临床特征,以期为拓宽Delta变异株分子结构功能变异研究方向,为未来COVID-19疫苗设计与应用提供思路。

Genomic Profile of SARS-COV-2 Associated with COVID-19 Outbreaks in N’Djamena, Chad

Background: SARS-CoV-2 has circulated worldwide with dramatic consequences. In Chad, we have no data reported of variants. The aim of this study was to identify the SARS-CoV-2 variants that circulated during the epidemic from 2020 to 2021. Methods: This is a cross-sectional, descriptive study carried out between 2020 and 2021. Samples from patients with suspected COVID-19 were tested in five laboratories in N’Djamena. One hundred quality samples of the positives were sequenced in Kinshasa using Oxford nanopore technologies minion and the Protocol Midnight SARS-CoV2. Data were processed using Excel version 16 software. Results: Of the 100 samples sequenced, 77 (77%) produced sequences, 23 (23%) did not. The genomic profiles were wild-type Wuhan and minor mutations (19A, 19B (A), 20A (B.1, B.2), 20B (AV.1), 20D (B.1.1.1 /C.36), 20C), variant of concern Alpha (20I), variant of concern Delta (21A/J), variant of interest Eta (21D), variant of concern Omicron (21K) and unclassified variant under surveillance (B.1.640). Of these variants, the maximums were detected in patients aged 26 - 35 with 30.26% and 25.26% in 36 - 45. However, 24.67% were in travelers and 75.32% in residents, 35.06% in those vaccinated against COVID-19 and 62.33% in non-vaccinates. The estimated case-fatality rate was 2.44% (107/4374). Conclusion: This work has provided preliminary data on COVID-19 and SARS-CoV-2 variants circulating during the 2020-2021 epidemics in Chad.

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.

Surveillance of emerging SARS-CoV-2 variants by nanopore technology-based genome sequencing

Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.

CRISPR-Cas12a-Empowered Electrochemical Biosensor for Rapid and Ultrasensitive Detection of SARS-CoV-2 Delta Variant

Coronavirus disease 2019(COVID-19)is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).The gold standard method for the diagnosis of SARS-CoV-2 depends on quantitative reverse transcription-polymerase chain reaction till now,which is time-consuming and requires expensive instrumentation,and the confirmation of variants relies on further sequencing techniques.Herein,we first proposed a robust technique-methodology of electrochemical CRISPR sensing with the advantages of rapid,highly sensitivity and specificity for the detection of SARS-CoV-2 variant.To enhance the sensing capability,gold electrodes are uniformly decorated with electro-deposited gold nanoparticles.Using DNA template identical to SARS-CoV-2 Delta spike gene sequence as model,our biosensor exhibits excellent analytical detection limit(50 fM)and high linearity(R2=0.987)over six orders of magnitude dynamic range from 100 fM to 10 nM without any nucleic-acid-amplification assays.The detection can be completed within 1 h with high stability and specificity which benefits from the CRISPR-Cas system.Furthermore,based on the wireless micro-electrochemical platform,the proposed biosensor reveals promising application ability in point-of-care testing.

A Retrospective Analysis of Wastewater Confirms Dominant Circulation of SARS-CoV-2 Delta Variant in Nairobi, Kenya, between April 2021 and August 2021

Wastewater surveillance has been applied in various parts of the world to monitor the introduction and transmissions of SARS-CoV-2 variants in a population. The knowledge of SARS-CoV-2 variants circulating in a population is critical to COVID-19 management and timing of the application of public health countermeasures. Contrary to the routine clinical surveillance of SARS-CoV-2 where cases from asymptomatic patients are often underreported, wastewater surveillance offers an unbiased tool for monitoring the extent of SARS-CoV-2 transmissions in a community. The present study aimed to characterize SARS-CoV-2 variants that circulated in Nairobi County, Kenya, between April 2021 and August 2021 utilizing wastewater samples. Viral RNA was extracted from wastewater samples, followed by SARS-CoV-2 screening by real-time RT-qPCR before targeted sequencing of the Spike gene. Forty samples were analyzed, of which 50% (n = 20) tested positive for SARS-CoV-2 by real-time RT-qPCR. Of these, 45% (n = 9) were successfully amplified by RT-PCR and sequenced. The majority (78%, 7/9) of the viruses belonged to the Delta (B.1.617.2) lineage of SARS-CoV-2, while a minority (22%) belonged to the Alpha (B.1.1.7) and Alpha-Delta lineages. Phylogenetic analysis of the SARS-COV-2 delta lineage strains revealed scattered clustering of the Kenyan viruses among the global strains included in the analysis, suggesting different introductory routes into the country. On the whole, our results confirm previous clinical findings that SARS-CoV-2 variants belonging to the Alpha (B.1.1.7) and Delta (B.1.617.2) lineages circulated in Nairobi County, Kenya during the study period, with the latter predominating. This is the first study to describe the diversity of SARS-CoV-2 variants circulating in Kenya, through wastewater analysis.

Case series in Indonesia:B.1.617.2(delta)variant of SARS-CoV-2 infection after a second dose of vaccine

BACKGROUND The B.1.617.2(delta)variant of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)was first discovered in Maharashtra in late 2020 and has rapidly expanded across India and worldwide.It took only 2 mo for this variant to spread in Indonesia,making the country the new epicenter of the delta variant as of July 2021.Despite efforts made by accelerating massive rollouts of current vaccines to protect against infection,cases of fully-vaccinated people infected with the delta variant have been reported.AIM To describe the demographic statistics and clinical presentation of the delta variant infection after the second dose of vaccine in Indonesia.METHODS A retrospective,single-centre case series of the general consecutive population that worked or studied at Faculty of Medicine,Universitas Indonesia with confirmed Delta Variant Infection after a second dose of vaccine from 24 June and 25 June 2021.Cases were collected retrospectively based on a combination of author recall,reverse transcription-polymerase chain reaction(RT-PCR),and whole genome sequencing results from the Clinical Microbiology Laboratory,Faculty of Medicine,Universitas Indonesia.RESULTS Between 24 June and 25 June 2021,15 subjects were confirmed with the B.1.617.2(delta)variant infection after a second dose of the vaccine.Fourteen subjects were vaccinated with CoronaVac(Sinovac)and one subject with ChAdOx1 nCoV-19(Oxford-AstraZeneca).All of the subjects remained in home isolation,with fever being the most common symptom at the onset of illness(n=10,66.67%).The mean duration of symptoms was 7.73 d(±5.444).The mean time that elapsed from the first positive swab to a negative RT-PCR test for SARS-CoV-2 was 17.93 d(±6.3464).The median time that elapsed from the second dose of vaccine to the first positive swab was 87 d(interquartile range:86-128).CONCLUSION Although this case shows that after two doses of vaccine,subjects are still susceptible to the delta variant infection,currently available vaccines remain the most effective protection.They reduce clinical manifestations of COVID-19,decrease recovery time from the first positive swab to negative swab,and lower the probability of hospitalization and mortality rate compared to unvaccinated individuals.

甘肃省SARS-CoV-2 Delta变异株感染的COVID-19流行病学和临床特征分析

目的分析新型冠状病毒(SARS-CoV-2)Delta变异株感染的新型冠状病毒肺炎(COVID-19)的流行病学及临床特征。方法回顾性分析2021年10月25日-11月19日兰州市第二人民医院雁滩分院收治的SARS-CoV-2 Delta变异株感染的本土138例COVID-19确诊患者的流行病学和临床特征,采集流行病学及人口学信息、临床症状、实验室检查、胸部CT、治疗和预后数据,最终随访日期为2021年11月27日。结果截至2021年11月19日,甘肃省此次疫情累计报告COVID-19确诊病例144例,其中兰州市第二人民医院雁滩分院集中收治138例,男65例(47.1%),女73例(52.9%),男女比例为1:1.12,年龄2~87(42.7±21.0)岁,临床分型以普通型(48.6%,67/138)为主。SARS-CoV-2 Delta变异株的传播方式以密闭空间为主,具有明显的旅行团聚集性和家庭聚集性;密切接触者筛查和社区排查是发现感染者的主要途径;86.2%(119/138)的确诊患者已接种国产COVID-19灭活疫苗;临床症状最常见的为咳嗽(57.2%,79/138),其次为咽痛(28.3%,39/138)、咽干(24.6%,34/138)、咳痰(21.0%,29/138)等,有发热症状的患者仅占20.3%(28/138),4例(2.9%)出现嗅觉、味觉减退或丧失。实验室检查血清淀粉样蛋白A和高密度脂蛋白胆固醇升高明显,SARS-CoV-2核酸检测ORF1ab基因Ct值为26.31±7.63,N基因为26.35±7.17;71.3%(72/101)的确诊患者胸部CT显示双侧肺叶受累,病灶位置以双肺下叶多见,病灶形态主要为片状、斑片状磨玻璃影。所有确诊患者均采用中西医结合治疗,以俯卧位通气和中医治疗为主,重症患者中医治疗率达100%,在呼吸支持、营养支持、抗凝的基础上配合中和抗体等免疫治疗。结论甘肃省SARS-CoV-2 Delta变异株感染的COVID-19确诊患者主要临床特征为发热比例低、病毒核酸转阴时间长、疫苗接种后重症风险低、治疗效果好,无插管,无体外膜肺氧合(ECMO),无死亡病例。“一人一方案”的中西医结合个性化治疗可有效控制病情进展,治愈疾病。

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.

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.

New and Newer Vaccines for SARS-CoV-2 Variants. Are the Major Vaccine Developers on the Right Track, Or Is Delipidation the Answer?

Background: Global Covid-19 pandemic has led to remarkable scientific achievements resulting in the development and rapid implementation of vaccines towards the original wild-type SARS-CoV-2 virus. Most Covid-19 vaccines are targeted to only one protein (the Spike protein) on the virus. SARS-CoV-2 that causes Covid-19 naturally undergoes multiple mutations over time. Such mutations can be inconsequential or have dire consequences. The lack of effectiveness of current vaccines towards mutated variants of Covid-19 is of major concern. The objective of this study is to describe an optimal solvent system that creates, via delipidation, a non-synthetic, host-derived or nonhost-derived modified viral particle that has its lipid envelope removed, exposing hidden undenatured proteins from within the virus, that generate a positive immunologic response when administered into a host, thereby providing a vaccine that offers strong and broad protection against the virus. Methods: Lipid removal from viruses by specific procedures renders the exposure of hidden proteins. Protection by antibodies to all of the virus’ protein types has shown to be far superior to protection by antibodies that are created by a single protein type. Results: Published studies with the Hepatitis virus, Pestivirus and HIV virus have reported the wide range of applications with this delipidation approach resulting in effectively long-term and broad protection vaccines. Conclusion: Mutations are rendering existing vaccines less effective. New approaches to obtain a more permanent vaccine that minimizes the effects of mutation are obtainable by delipidation of the viral particle and thereby creating vaccines that are more permanent with broad protection.

Epidemiology of SARS-CoV-2 and Emergence of UK Variant in Zintan City of Libya

Introduction: Coronavirus Disease 2019 (COVID-19) is an infectious respiratory disease caused by SARS-CoV-2. The disease was first broke out in Wuhan City, Hubei Province, China and subsequently spread to all countries and was considered by WHO as a worldwide pandemic. This study is aimed to determine the epidemiology of SARS-CoV-2 and the presence of UK variants in Zintan city of Libya taking some risk factors into account. Methods: In a cross-sectional retrospective study, a total of 15486 nasopharyngeal swabs were collected from COVID-19 suspected patients, travelers and people need disease-free certificates for hospital admission, etc. The samples were collected during the period from August 2020 to June 2021 and tested using real-time RT-PCR (rRT-PCR) kits for SARS-CoV-2 and UK variants. Age groups, sex, and monthly weather were considered as risk factors. Results: The positivity rate of COVID-19 in Zintan city was estimated to be (3891;25.12%) for the period from August 2020 to June 2021. Females showed significantly (p < 0.05) higher positivity rate (2100;54%) as compared to males (1791;46%). Out of the 3891 positive cases, 52 were deceased. The Case Fatality Rate (CFR) was 1.33 recorded significantly in cases aged ≥ 65 years which was higher in males (56.66%) than females (43.33%). The peak of the first wave of infection was recorded in October 2020 (590;15.15%) whereas the peak of the second wave of infection was recorded in April 2021 (727;18.71%). The positivity rate was decreased as the temperature increased. UK variant is detected firstly in May 2021 with the percentage of 6.2% of tested samples. Conclusions: Health Authorities are encouraged to continue implementing the control measures during the decrease phase of infection to stop transmission of the virus in the next wave. Early detection of new variants and studying their genetic characteristics play a valuable role in prevention and control.

SARS-CoV-2 Omicron variant (B.1.1.529): A concern with immune escape

Omicron,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variant that is now spreading across the world,is the most altered version to emerge so far,with mutations comparable to changes reported in earlier variants of concern linked with increased transmissibility and partial resistance to vaccineinduced immunity.This article provides an overview of the SARS-CoV-2 variant Omicron(B.1.1.529)by reviewing the literature from major scientific databases.Although clear immunological and clinical data are not yet available,we extrapolated from what is known about mutations present in the Omicron variant of SARS-CoV-2 and offer preliminary indications on transmissibility,severity,and immune escape through existing research and databases.

新型冠状病毒Delta变异株危重型患者合并急性鼻窦炎的临床特点及CT表现

目的 探讨新型冠状病毒(severeacute respiratory syndrome coronavirus2,SARS-Co V-2)Delta变异株危重型患者合并急性鼻窦炎的临床特点及CT表现。方法采用回顾性研究收集2021年5月21日至2021年7月7日,广州医科大学附属市八医院收治的11例SARS-Co V-2 D e l ta变异株危重型合并急性鼻窦炎患者为研究对象,对其临床特点及鼻窦CT影像资料进行分析。结果 11例SARS-Co V-2Delta变异株感染的危重型患者中,男性7例,女性4例,年龄75(66,85)岁,合并基础疾病100%(11/11),发热100%(11/11),鼻腔黏膜充血水肿100%(11/11),鼻腔内分泌物100%(11/11),鼻窦合并细菌感染72.7%(8/11),合并真菌感染9.1%(1/11),合并细菌及真菌混合感染18.2%(2/11),C-反应蛋白(CRP)117.71(61.08,159.65)mg/L,血清淀粉样蛋白A(SSA)296.48(246.11,306.30)mg/L,白细胞(WBC)10.12(8.35,10.49)×109/L,嗜中性粒细胞(NEU)7.7(5.78,8.27)×109/L,淋巴细胞(LYM)1.00(0.62,1.24)×109/L,降钙素(PCT)0.30(0.23,0.45)ng/m L,白细胞介素-6(IL-6)234.4(176.7,271.41)pg/m L,11例鼻窦炎患者应用鼻-鼻窦炎Lund-Mackay评分标准CT评分为20(17.5,21)分。结论 SARS-Co V-2 Delta变异株危重型合并鼻窦炎的患者均为老年人,鼻窦可以合并细菌、真菌感染,以细菌感染为主,常伴各项炎性指标的升高,以合并基础疾病、发热、鼻腔黏膜充血水肿、鼻腔内分泌物为主要临床表现,副鼻窦CT以窦腔内液性低密度影主要表现,炎性分泌物可阻塞窦口鼻道复合体,当SARS-Co V-2 Delta变异株患者外周血炎性指标明显升高并鼻腔黏膜充血水肿及分泌物时,应及时行鼻窦CT扫描,当CT显示窦腔内液性低密度影时,可提示临床急性鼻窦炎并及时干预治疗,以降低其发展至严重并发症的风险。

Multi-omics analysis of attenuated variant reveals potential evaluation marker of host damaging for SARS-CoV-2 variants

SARS-CoV-2 continues to threaten human society by generating novel variants via mutation and recombination.The high number of mutations that appeared in emerging variants not only enhanced their immune-escaping ability but also made it difficult to predict the pathogenicity and virulence based on viral nucleotide sequences.Molecular markers for evaluating the pathogenicity of new variants are therefore needed.By comparing host responses to wild-type and variants with attenuated pathogenicity at proteome and metabolome levels,six key molecules on the polyamine biosynthesis pathway including putrescine,SAM,dc-SAM,ODC1,SAMS,and SAMDC were found to be differentially upregulated and associated with pathogenicity of variants.To validate our discovery,human airway organoids were subsequently used which recapitulates SARS-CoV-2 replication in the airway epithelial cells of COVID-19 patients.Using ODC1 as a proof-ofconcept,differential activation of polyamine biosynthesis was found to be modulated by the renin-angiotensin system(RAS)and positively associated with ACE2 activity.Further experiments demonstrated that ODC1 expression could be differentially activated upon a panel of SARS-CoV-2 variants of concern(VOCs)and was found to be correlated with each VOCs’pathogenic properties.Particularly,the presented study revealed the discriminative ability of key molecules on polyamine biosynthesis as a predictive marker for virulence evaluation and assessment of SARS-CoV-2 variants in cell or organoid models.Our work,therefore,presented a practical strategy that could be potentially applied as an evaluation tool for the pathogenicity of current and emerging SARS-CoV-2 variants.

SARS-CoV-2 variants are associated with different clinical courses in children with MIS-C

Background Recent infection with SARS‑CoV-2 in children has been associated with multisystem inflammatory syndrome in children(MIS-C).SARS‑CoV-2 has undergone different mutations.Few publications exist about specific variants and their correlation with the severity of MIS-C.Methods This was a single-center,retrospective study including all patients admitted with MIS-C at Rady Children’s Hospital-San Diego between May 2020 and March 2022.Local epidemiologic data,including viral genomic information,were obtained from public records.Demographics,clinical presentation,laboratory values,and outcomes were obtained from electronic medical records.Results The analysis included 104 pediatric patients.Four MIS-C waves were identified.Circulating variants in San Diego during the first wave included clades 20A to C.During the second wave,there were variants from clades 20A to C,20G,21C(Epsilon),20I(Alpha),and 20J(Gamma).The third wave had Delta strains(clades 21A,21I,and 21J),and the fourth had Omicron variants(clades 21K,21L,and 22C).MIS-C presented with similar symptoms and laboratory findings across all waves.More patients were admitted to the pediatric intensive care unit(PICU)(74%)and required inotropic support(63%)during the second wave.None of the patients required mechanical circulatory support,and only two required invasive ventilatory support.There was no mortality.Conclusions The various strains of SARS-CoV-2 triggered MIS-C with differing severities,with the second wave having a more severe clinical course.Whether the differences in disease severity across variants were due to changes in the virus or other factors remains unknown.

Development of T cell antigen-based human coronavirus vaccinesagainst nAb-escaping SARS-CoV-2 variants

Currently approved vaccines have been successful in preventing the severity of COVID-19 and hospitalization. These vaccines primarily induce humoral immune responses;however, highly transmissible and mutated variants, such as the Omicron variant, weaken the neutralization potential of the vaccines, thus,raising serious concerns about their efficacy. Additionally, while neutralizing antibodies(nAbs) tend to wane more rapidly than cell-mediated immunity, long-lasting T cells typically prevent severe viral illness by directly killing infected cells or aiding other immune cells. Importantly, T cells are more cross-reactive than antibodies, thus, highly mutated variants are less likely to escape lasting broadly cross-reactive T cell immunity. Therefore, T cell antigen-based human coronavirus(HCoV) vaccines with the potential to serve as a supplementary weapon to combat emerging SARS-CoV-2 variants with resistance to n Abs are urgently needed. Alternatively, T cell antigens could also be included in B cell antigen-based vaccines to strengthen vaccine efficacy. This review summarizes recent advancements in research and development of vaccines containing T cell antigens or both T and B cell antigens derived from proteins of SARS-CoV-2 variants and/or other HCo Vs based on different vaccine platforms.

Identification of druggable host dependency factors shared by multiple SARS-CoV-2 variants of concern

The high mutation rate of SARS-CoV-2 leads to the emergence of multiple variants,some of which are resistant to vaccines and drugs targeting viral elements.Targeting host dependency factors,e.g.cellular proteins required for viral replication,would help prevent the development of resistance.However,it remains unclear whether different SARS-CoV-2 variants induce conserved cellular responses and exploit the same core host factors.To this end,we compared three variants of concern and found that the host transcriptional response was conserved,differing only in kinetics and magnitude.Clustered regularly interspaced short palindromic repeats screening identified host genes required for each variant during infection.Most of the genes were shared by multiple variants.We validated our hits with small molecules and repurposed the US Food and Drug Administration-approved drugs.All the drugs were highly active against all the tested variants,including new variants that emerged during the study(Delta and Omicron).Mechanistically,we identified reactive oxygen species production as a key step in early viral replication.Antioxidants such as N-acetyl cysteine(NAC)were effective against all the variants in both human lung cells and a humanized mouse model.Our study supports the use of available antioxidant drugs,such as NAC,as a general and effective anti-COVID-19 approach.