Development of a model by LASSO to predict hospital length of stay (LOS) in patients with the SARS-Cov-2 omicron variant.

The length of stay (LOS) in hospital varied considerably in different patients with COVID-19 caused by SARS-CoV-2 Omicron variant. The study aimed to explore the clinical characteristics of Omicron patients, identify prognostic factors, and develop a prognostic model to predict the LOS of Omicron patients. This was a single center retrospective study in a secondary medical institution in China. A total of 384 Omicron patients in China were enrolled. According to the analyzed data, we employed LASSO to select the primitive predictors. The predictive model was constructed by fitting a linear regression model using the predictors selected by LASSO. Bootstrap validation was used to test performance and eventually we obtained the actual model. Among these patients, 222 (57.8%) were female, the median age of patients was 18 years and 349 (90.9%) completed two doses of vaccination. Patients on admission diagnosed as mild were 363 (94.5%). Five variables were selected by LASSO and a linear model, and those with P < 0.05 were integrated into the analysis. It shows that if Omicron patients receive immunotherapy or heparin, the LOS increases by 36% or 16.1%. If Omicron patients developed rhinorrhea or occur familial cluster, the LOS increased by 10.4% or 12.3%, respectively. Moreover, if Omicron patients' APTT increased by one unit, the LOS increased by 0.38%. Five variables were identified, including immunotherapy, heparin, familial cluster, rhinorrhea, and APTT. A simple model was developed and evaluated to predict the LOS of Omicron patients. The formula is as follows: Predictive LOS = exp(1*2.66263 + 0.30778*Immunotherapy + 0.1158*Familiar cluster + 0.1496*Heparin + 0.0989*Rhinorrhea + 0.0036*APTT).

Longitudinal neutralization activities on authentic Omicron variant provided by three doses of BBIBP-CorV vaccination during one year.

The majority of people in China have been immunized with the inactivated viral vaccine BBIBP-CorV. The emergence of the Omicron variant raised the concerns about protection efficacy of the inactivated viral vaccine in China. However, longitudinal neutralization data describing protection efficacy against Omicron variant is still lacking. Here we present one-year longitudinal neutralization data of BBIBP-CorV on authentic Omicron, Delta, and wild-type strains using 224 sera collected from 14 volunteers who have finished three doses BBIBP-CorV. The sera were also subjected for monitoring the SARS-CoV-2 specific IgG, IgA, and IgM responses on protein and peptide microarrays. The neutralization titers showed different protection efficacies against the three strains. By incorporating IgG and IgA signals of proteins and Spike protein derived peptide on microarray, panels as potential surrogate biomarkers for rapid estimation of neutralization titers were established. These data support the necessity of the 3rd dose of BBIBP-CorV vaccination. After further validation and assay development, the panels could be used for reliable, convenient and fast evaluation of the efficacy of vaccination.

AabHLH113 integrates jasmonic acid and abscisic acid signaling to positively regulate artemisinin biosynthesis in Artemisia annua.

Artemisinin, a sesquiterpene lactone isolated from Artemisia annua, is in huge market demand due to its efficient antimalarial action, especially after the COVID-19 pandemic. Many researchers have elucidated that phytohormones jasmonic acid (JA) and abscisic acid (ABA) positively regulate artemisinin biosynthesis via types of transcription factors (TFs). However, the crosstalk between JA and ABA in regulating artemisinin biosynthesis remains unclear. Here, we identified a novel ABA- and JA-induced bHLH TF, AabHLH113, which positively regulated artemisinin biosynthesis by directly binding to the promoters of artemisinin biosynthetic genes, DBR2 and ALDH1. The contents of artemisinin and dihydroartemisinic acid increased by 1.71- to 2.06-fold and 1.47- to 2.23-fold, respectively, in AabHLH1113 overexpressed A. annua, whereas they decreased by 14-36% and 26-53%, respectively, in RNAi-AabHLH113 plants. Furthermore, we demonstrated that AabZIP1 and AabHLH112, which, respectively, participate in ABA and JA signaling pathway to regulate artemisinin biosynthesis, directly bind to and activate the promoter of AabHLH113. Collectively, we revealed a complex network in which AabHLH113 plays a key interrelational role to integrate ABA- and JA-mediated regulation of artemisinin biosynthesis.

A luciferase based automated assay for rapid and sensitive detection of SARS-CoV-2 antibodies.

The Coronavirus disease 2019 (COVID-19) pandemic brings great challenges to the public health and social economics around the world. As the pandemic continues and the mass vaccination goes on, monitoring the antibodies is particularly important for the epidemiological survey and vaccine assessment. Here, we developed a luciferase immunoprecipitation assay combined with an automated platform to detect anti-Receptor Binding Domain (RBD) antibody, where protein A and protein G modified magnetic beads were used to capture antibodies in serum samples and SARS-CoV-2 RBD was fused with Gaussia luciferase to label the captured target antibodies. The whole detection procedure can be completed within 20 min. The developed assay has proven up to 32 times more sensitive than ELISA for the detection of RBD antibodies. Furthermore, the results of the antibody detection of sera from vaccination as well as convalescence displayed good performance. The automated platform may provide a powerful tool for the control of COVID-19 pandemic by vaccination and the research of SARS-CoV-2 seroconversion.

Comparison of clinical characteristics between SARS-CoV-2 Omicron variant and Delta variant infections in China.

Background: The continued 'evolution' of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the emergence of the Omicron variant after the Delta variant, resulting in a significant increase in the number of people with COVID-19. This increase in the number of cases continues to have a significant impact on lives. Therefore, a more detailed understanding of the clinical characteristics of Omicron infection is essential. Methods: Using medical charts, we extracted clinical information for 384 patients infected with the Omicron variant in Anyang City, Henan Province, China. Epidemiology and clinical characteristics were compared with a cohort of people infected with the Delta variant in Zhengzhou in 2021. Findings: Common initial symptoms at onset of illness were cough [240 (63%)], expectoration [112 (29%)], fever [96 (25%)], nasal congestion [96 (25%)] and myalgia or fatigue [30 (6%)]. In patients with the Omicron variant, levels of total cholesterol, low-density lipoprotein and creatinine increased in 52 (14%), 36 (9%) and 58 (15%) patients, respectively, compared with patients with the Delta variant [one (1%), one (1%) and two (2%)]. Levels of triglyceride and high-density lipoprotein also increased. In patients with the Omicron variant, the levels of specific gravity and the erythrocyte sedimentation rate were increased in 115 (30%) and 81 (21%) patients, and serum levels of complement 3 decreased in 93 (41%). Results: Compared with patients infected with Delta, no major differences in initial clinical symptoms were identified in patients infected with Omicron. However, dyslipidemia and kidney injury were much more severe in patients with the Omicron variant, and the erythrocyte sedimentation rate was increased. Due to decreased levels of complement 3, the immunity of patients with the Omicron variant was weak.

Comparison of clinical characteristics between SARS-CoV-2 Omicron variant and Delta variant infections in China

Background The continued ‘evolution’ of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the emergence of the Omicron variant after the Delta variant, resulting in a significant increase in the number of people with COVID-19. This increase in the number of cases continues to have a significant impact on lives. Therefore, a more detailed understanding of the clinical characteristics of Omicron infection is essential. Methods Using medical charts, we extracted clinical information for 384 patients infected with the Omicron variant in Anyang City, Henan Province, China. Epidemiology and clinical characteristics were compared with a cohort of people infected with the Delta variant in Zhengzhou in 2021. Findings Common initial symptoms at onset of illness were cough [240 (63%)], expectoration [112 (29%)], fever [96 (25%)], nasal congestion [96 (25%)] and myalgia or fatigue [30 (6%)]. In patients with the Omicron variant, levels of total cholesterol, low-density lipoprotein and creatinine increased in 52 (14%), 36 (9%) and 58 (15%) patients, respectively, compared with patients with the Delta variant [one (1%), one (1%) and two (2%)]. Levels of triglyceride and high-density lipoprotein also increased. In patients with the Omicron variant, the levels of specific gravity and the erythrocyte sedimentation rate were increased in 115 (30%) and 81 (21%) patients, and serum levels of complement 3 decreased in 93 (41%). Results Compared with patients infected with Delta, no major differences in initial clinical symptoms were identified in patients infected with Omicron. However, dyslipidemia and kidney injury were much more severe in patients with the Omicron variant, and the erythrocyte sedimentation rate was increased. Due to decreased levels of complement 3, the immunity of patients with the Omicron variant was weak.

Shared IGHV1-69-encoded neutralizing antibodies contribute to the emergence of L452R substitution in SARS-CoV-2 variants.

SARS-CoV-2 variants continue to emerge facing established herd immunity. L452R, previously featured in the Delta variant, quickly emerged in Omicron subvariants, including BA.4/BA.5, implying a continued selection pressure on this residue. The underlying links between spike mutations and their selective pressures remain incompletely understood. Here, by analyzing 221 structurally characterized antibodies, we found that IGHV1-69-encoded antibodies preferentially contact L452 using germline-encoded hydrophobic residues at the tip of HCDR2 loop. Whereas somatic hypermutations or VDJ rearrangements are required to acquire L452-contacting hydrophobic residues for non-IGHV1-69 encoded antibodies. Antibody repertoire analysis revealed that IGHV1-69 L452-contacting antibody lineages are commonly induced among COVID-19 convalescents but non-IGHV1-69 encoded antibodies exhibit limited prevalence. In addition, we experimentally demonstrated that L452R renders most published IGHV1-69 antibodies ineffective. Furthermore, we found that IGHV1-69 L452-contacting antibodies are enriched in convalescents experienced Omicron BA.1 (without L452R) breakthrough infections but rarely found in Delta (with L452R) breakthrough infections. Taken together, these findings support that IGHV1-69 population antibodies contribute to selection pressure for L452 substitution. This study thus provides a better understanding of SARS-CoV-2 variant genesis and immune evasion.

SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope.

Population antibody response is thought to be important in selection of virus variants. We report that SARS-CoV-2 infection elicits a population immune response that is mediated by a lineage of VH1-69 germline antibodies. A representative antibody R1-32 from this lineage was isolated. By cryo-EM, we show that it targets a semi-cryptic epitope in the spike receptor-binding domain. Binding to this non-ACE2 competing epitope results in spike destruction, thereby inhibiting virus entry. On the basis of epitope location, neutralization mechanism and analysis of antibody binding to spike variants, we propose that recurrent substitutions at 452 and 490 are associated with immune evasion of the identified population antibody response. These substitutions, including L452R (present in the Delta variant), disrupt interactions mediated by the VH1-69-specific hydrophobic HCDR2 to impair antibody-antigen association, enabling variants to escape. The first Omicron variants were sensitive to antibody R1-32 but subvariants that harbour L452R quickly emerged and spread. Our results provide insights into how SARS-CoV-2 variants emerge and evade host immune responses.

Increased pathogenicity and aerosol transmission for one SARS-CoV-2 B.1.617.2 Delta variant over the wild-type strain in hamsters.

During the two-year pandemic of coronavirus disease 2019 (COVID-19), its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been evolving. SARS-CoV-2 Delta, a variant of concern, has become the dominant circulating strain worldwide within just a few months. Here, we performed a comprehensive analysis of a new B.1.617.2 Delta strain (Delta630) compared with the early WIV04 strain (WIV04) in vitro and in vivo, in terms of replication, infectivity, pathogenicity, and transmission in hamsters. When inoculated intranasally, Delta630 led to more pronounced weight loss and more severe disease in hamsters. Moreover, 40% mortality occurred about one week after infection with 104 PFU of Delta630, whereas no deaths occurred even after infection with 105 PFU of WIV04 or other strains belonging to the Delta variant. Moreover, Delta630 outgrew over WIV04 in the competitive aerosol transmission experiment. Taken together, the Delta630 strain showed increased replication ability, pathogenicity, and transmissibility over WIV04 in hamsters. To our knowledge, this is the first SARS-CoV-2 strain that causes death in a hamster model, which could be an asset for the efficacy evaluation of vaccines and antivirals against infections of SARS-CoV-2 Delta strains. The underlying molecular mechanisms of increased virulence and transmission await further analysis.

Ultrasensitive monitoring of SARS-CoV-2-specific antibody responses based on a digital approach reveals one week of IgG seroconversion.

COVID-19 is still unfolding, while many people have been vaccinated. In comparison to nucleic acid testing (NAT), antibody-based immunoassays are faster and more convenient. However, its application has been hampered by its lower sensitivity and the existing fact that by traditional immunoassays, the measurable seroconversion time of pathogen-specific antibodies, such as IgM or IgG, lags far behind that of nucleic acids. Herein, by combining the single molecule array platform (Simoa), RBD, and a previously identified SARS-CoV-2 S2 protein derivatized 12-aa peptide (S2-78), we developed and optimized an ultrasensitive assay (UIM-COVID-19 assay). Sera collected from three sources were tested, i.e., convalescents, inactivated virus vaccine-immunized donors and wild-type authentic SARS-CoV-2-infected rhesus monkeys. The sensitivities of UIM-COVID-19 assays are 100-10,000 times higher than those of conventional flow cytometry, which is a relatively sensitive detection method at present. For the established UIM-COVID-19 assay using RBD as a probe, the IgG and IgM seroconversion times after vaccination were 7.5 and 8.6 days vs. 21.4 and 24 days for the flow cytometry assay, respectively. In addition, using S2-78 as a probe, the UIM-COVID-19 assay could differentiate COVID-19 patients (convalescents) from healthy people and patients with other diseases, with AUCs ranging from 0.85-0.95. In summary, the UIM-COVID-19 we developed here is a promising ultrasensitive biodetection strategy that has the potential to be applied for both immunological studies and diagnostics.

A modified nutrition risk screening 2002 predicts the risk of death among hospitalized patients with COVID-19.

OBJECTIVES: The aim of this study was to evaluate the ability of a modified Nutrition Risk Screening 2002 (modified NRS) compared with other nutrition screening tools such as NRS 2002, Mini Nutrition Assessment Short Form (MNA-SF), and Malnutrition Universal Screening Tool (MUST) on predicting the risk of death in patients with coronavirus disease 2019 (COVID-19). METHODS: We retrospectively collected data of patients who were admitted to the West campus of Union Hospital, Tongji Medical College, Huazhong University of Science and Technology between January 25th, 2020 to April 24th, 2020. The nutritional status of the patients was assessed by modified NRS, NRS 2002, MNA-SF, and MUST. According to the score of modified NRS, patients were divided into malnutrition risk group (score ≥3) and normal nutrition group (score <3). Clinical characteristics were compared between the two groups. Kaplan meier survival curve was used to analyze the difference of compositing survival rate between the two groups. The predictive efficacy of different nutritional scales on the outcome of death was detected by Receiver operating characteristic (ROC) analysis. RESULTS: The modified NRS, NRS 2002, MNA-SF, and MUST identified malnutrition risk in 71.4%, 57.9%, 73.9%, and 43.4% of the patients, respectively. The patients were divided into malnutrition risk group and normal nutrition group by modified NRS score. Patients in the malnutrition risk group were older (65 y vs. 56 y) and with more severe and critical cases (42.30% vs. 5.20%) and diabetes cases (21.50% vs. 9.80%), worse prognosis (death of 13.80% vs. 0.50%), longer hospital stay (29 days vs. 23 days), lower albumin (31.85 g/L vs. 38.55 g/L) and prealbumin (201.95 mg/L vs. 280.25 mg/L) compared with the normal nutrition group (P were <0.001, respectively). There were more patients with chronic respiratory disease in malnutrition risk group (9.70 vs. 2.10%, P = 0.001). BMI was lower in malnutrition risk group (23.45 kg/m2vs. 24.15 kg/m2, P = 0.017). Kaplan meier survival curve demonstrated that the survival of malnutrition risk group was significantly lower than normal nutrition group (P < 0.001). The area under the ROC curve (AUC) of the modified NRS scale (0.895) outperformed NRS 2002 (0.758), MNA-SF (0.688), and MUST (0.485). The former three scales could predict the risk of death (P were < 0.001), while MUST could not (P = 0.690). CONCLUSIONS: Patients with COVID-19 at risk of malnutrition have a worse prognosis than those with normal nutrition. The modified NRS scale could effectively predict the risk of death among patients with COVID-19.

A Class of Shark-Derived Single-Domain Antibodies can Broadly Neutralize SARS-Related Coronaviruses and the Structural Basis of Neutralization and Omicron Escape.

The identification of a novel class of shark-derived single domain antibodies, named vnarbodies that show picomolar affinities binding to the receptor binding domain (RBD) of Wuhan and Alpha, Beta, Kappa, Delta, Delta-plus, and Lambda variants, is reported. Vnarbody 20G6 and 17F6 have broad neutralizing activities against all these SARS-CoV-2 viruses as well as other sarbecoviruses, including Pangolin coronavirus and Bat coronavirus. Intranasal administration of 20G6 effectively protects mice from the challenges of SARS-CoV-2 Wuhan and Beta variants. 20G6 and 17F6 contain a unique "WXGY" motif in the complementary determining region 3 that binds to a hidden epitope on RBD, which is highly conserved in sarbecoviruses through a novel ß-sheet interaction. It is found that the S375F mutation on Omicron RBD disrupts the structure of ß-strand, thus impair the binding with 20G6. The study demonstrates that shark-derived vnarbodies offer a prophylactic and therapeutic option against most SARS-CoV-2 variants and provide insights into antibody evasion by the Omicron variant.

The emerging roles of retromer and sorting nexins in the life cycle of viruses.

Retromer and sorting nexins (SNXs) transport cargoes from endosomes to the trans-Golgi network or plasma membrane. Recent studies have unveiled the emerging roles for retromer and SNXs in the life cycle of viruses, including members of Coronaviridae, Flaviviridae and Retroviridae. Key components of retromer/SNXs, such as Vps35, Vps26, SNX5 and SNX27, can affect multiple steps of the viral life cycle, including facilitating the entry of viruses into cells, participating in viral replication, and promoting the assembly of virions. Here we present a comprehensive updated review on the interplay between retromer/SNXs and virus, which will shed mechanistic insights into controlling virus infection.

Analysis of B Cell Receptor Repertoires Reveals Key Signatures of the Systemic B Cell Response after SARS-CoV-2 Infection.

A comprehensive study of the B cell response against SARS-CoV-2 could be significant for understanding the immune response and developing therapeutical antibodies and vaccines. To define the dynamics and characteristics of the antibody repertoire following SARS-CoV-2 infection, we analyzed the mRNA transcripts of immunoglobulin heavy chain (IgH) repertoires of 24 peripheral blood samples collected between 3 and 111 days after symptom onset from 10 COVID-19 patients. Massive clonal expansion of naive B cells with limited somatic hypermutation (SHM) was observed in the second week after symptom onset. The proportion of low-SHM IgG clones strongly correlated with spike-specific IgG antibody titers, highlighting the significant activation of naive B cells in response to a novel virus infection. The antibody isotype switching landscape showed a transient IgA surge in the first week after symptom onset, followed by a sustained IgG elevation that lasted for at least 3 months. SARS-CoV-2 infection elicited poly-germ line reactive antibody responses. Interestingly, 17 different IGHV germ line genes recombined with IGHJ6 showed significant clonal expansion. By comparing the IgH repertoires that we sequenced with the 774 reported SARS-CoV-2-reactive monoclonal antibodies (MAbs), 13 shared spike-specific IgH clusters were found. These shared spike-specific IgH clusters are derived from the same lineage of several recently published neutralizing MAbs, including CC12.1, CC12.3, C102, REGN10977, and 4A8. Furthermore, identical spike-specific IgH sequences were found in different COVID-19 patients, suggesting a highly convergent antibody response to SARS-CoV-2. Our analysis based on sequencing antibody repertoires from different individuals revealed key signatures of the systemic B cell response induced by SARS-CoV-2 infection. IMPORTANCE Although the canonical delineation of serum antibody responses following SARS-CoV-2 infection has been well established, the dynamics of antibody repertoire at the mRNA transcriptional level has not been well understood, especially the correlation between serum antibody titers and the antibody mRNA transcripts. In this study, we analyzed the IgH transcripts and characterized the B cell clonal expansion and differentiation, isotype switching, and somatic hypermutation in COVID-19 patients. This study provided insights at the repertoire level for the B cell response after SARS-CoV-2 infection.

Disrupted rhythms of life, work and entertainment and their associations with psychological impacts under the stress of the COVID-19 pandemic: A survey in 5854 Chinese people with different sociodemographic backgrounds

Background & aim: The coronavirus disease 2019 (COVID-19) pandemic has affected the life and work of people worldwide. The present study aimed to evaluate the rhythm disruptions of life, work, and entertainment, and their associations with the psychological impacts during the initial phase of the COVID-19 pandemic. Method: A cross-sectional study was conducted from the 10th to 17th March 2020 in China. A structured e-questionnaire containing general information, the Chinese version of Brief Social Rhythm Scale, and Zung's self-rating scales of depression and anxiety (SDS and SAS) was posted and collected online through a public media (i.e. EQxiu online questionnaire platform). Scores in sleeping, getting up, and socializing (SGS) rhythm and eating, physical practice, and entertainment (EPE) rhythm were compared among and between participants with different sociodemographic backgrounds including gender, age, education, current occupation, annual income, health status, and chronic disease status. Correlations of SDS and SAS with SGS-scale and EPE-scale were also analyzed. Results: Overall, 5854 participants were included. There were significant differences in the scores of SGS-scale and EPE-scale among people with different sociodemographic backgrounds. The scores were significantly higher in the groups with female gender, low education level, lower or higher than average income, poor health status, ages of 26-30 years or older than 61 years, nurses and subjects with divorce or widow status. There were also significant differences in SAS and SDS scores among people with different sociodemographic backgrounds (all P< 0.05). The overall prevalence of depression and anxiety was 24.3% and 12.6%, respectively, with nurses having the highest rates of depression (32.94%) and anxiety (18.98%) among the different occupational groups. SGS-scale was moderately correlated with SDS and SAS, and disruption of SGS rhythm was an independent risk factor for depression and anxiety. Conclusion: Social rhythm disruption was independently associated with depression and anxiety. Interventions should be applied to people vulnerable to the rhythm disruption during the COVID-19 pandemic. (PsycInfo Database Record (c) 2022 APA, all rights reserved)

Steep Decline in Binding Capability of SARS-CoV-2 Omicron Variant (B.1.1.529) RBD to the Antibodies in Early COVID-19 Convalescent Sera and Inactivated Vaccine Sera.

A new SARS-CoV-2 variant B.1.1.529 was named by the WHO as Omicron and classified as a Variant of Concern (VOC) on 26 November 2021. Because this variant has more than 50 mutations, including 30 mutations on the spike, it has generated a lot of concerns on the potential impacts of the VOC on COVID-19. Here through ELISA assays using the recombinant RBD proteins with sequences the same to that of SARS-CoV-2 WIV04 (lineage B.1), the Delta variant and the Omicron variant as the coating antigens, the binding capabilities between the RBDs and the antibodies in COVID-19 convalescent sera and vaccine sera after two doses of the inactivated vaccine produced by Sinopharm WIBP are compared with each other. The results showed that the Omicron variant may evade antibodies induced by the ancestral strain and by the inactivated vaccine, with significant reduction in the binding capability of its RBD much greater than that of the Delta variant.

A time series representation of protein sequences for similarity comparison.

Based on the physicochemical indexes of 20 amino acids and the Hungarian algorithm, each amino acid was mapped into a vector. And, the protein sequence can be represented as time series in eleven-dimensional space. In addition, the DTW algorithm was applied to calculate the distance between two time series to compare the similarities of protein sequences. The validity and accuracy of this method was illustrated by similarity comparison of ND5 proteins of nine species. Furthermore, homology analysis of eleven ACE2 proteins, which included human, Malayan pangolin and six species of bats, confirmed that the human had shorter evolutionary distance from the pangolin than those bats. The phylogenetic tree of spike protein sequences of 36 coronaviruses, which were divided into five groups, Class I, Class II, Class III, SARS-CoVs and COVID-19, was constructed.

Cost-effectiveness analysis of quadrivalent seasonal influenza vaccines in Beijing: A modeling analysis.

BACKGROUND: Since 2007, Beijing has offered a free trivalent influenza vaccine (TIV) for residents aged ≥ 60 years and school students. The quadrivalent influenza vaccine (QIV) was administered to school children in 2018 and will be administered to elderly adults in the future. In addition, health care workers (HCWs) who are involved in the prevention and control of COVID-19 were included in the program in 2020. This study aimed to analyze the cost-effectiveness of a comprehensive list of combined strategies of TIV and QIV for school children, elderly adults, and HCWs to identify the most cost-effective strategy. METHODS: A decision tree was developed to compare 1-year outcomes of TIV vs. QIV in three risk groups: school children, elderly adults, and HCWs. The outcome was incremental cost per quality-adjusted life-year (QALY). Probabilistic sensitivity analyses and scenario analyses were developed to assess the robustness of the results. RESULTS: From the perspective of society, this study found that the introduction of QIVs can be cost-effective for any and all targeted groups with a willingness-to-pay threshold of 3-fold GDP per capita. Among all programs, program H (all school children, elderly adults, and HCWs received the QIV) showed a 79% probability of being cost-effective with an incremental cost-effectiveness ratio (ICER) of 13,580 (95% CI: 13,294, 13,867) US$/QALY and was the preferred option in the base case scenario. CONCLUSION: The introduction of QIVs to school children, elderly adults, or HCWs is likely to be cost-effective, either separately or collectively. The introduction of QIV to school children, elderly adults, and health care workers simultaneously showed the highest probability of being cost-effective and was the preferred option.

Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern.

With the emergence and wide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs), such as the Delta variant (B.1.617.2 lineage and AY sublineage), it is important to track VOCs for sourcing of transmission. Currently, whole-genome sequencing is commonly used for detecting VOCs, but this is limited by the high costs of reagents and sophisticated sequencers. In this study, common mutations in the genomes of SARS-CoV-2 VOCs were identified by analyzing more than 1 million SARS-CoV-2 genomes from public data. Among them, mutations C1709A (a change of C to A at position 1709) and C56G, respectively, were found in more than 99% of the genomes of Alpha and Delta variants and were specific to them. Then, a method using the amplification refractory mutation system combined with quantitative reverse transcription-PCR (ARMS-RT-qPCR) based on the two mutations was developed for identifying both VOCs. The assay can detect as little as 1 copy/µL of the VOCs, and the results for identifying Alpha and Delta variants in clinical samples by the ARMS-RT-qPCR assay showed 100% agreement with the results using sequencing-based methods. The whole assay can be completed in 2.5 h using commercial fluorescent PCR instruments. Therefore, the ARMS-RT-qPCR assay could be used for screening the two highly concerning variants Alpha and Delta by normal PCR laboratories in airports and in hospitals and other health-related organizations. Additionally, based on the unique mutations identified by the genomic analysis, similar molecular assays can be developed for rapid identification of other VOCs. IMPORTANCE The current stage of the pandemic, led by SARS-CoV-2 variants of concern (VOCs), underscores the necessity to develop a cost-effective and rapid molecular diagnosis assay to differentiate the VOCs. In this study, over 1 million SARS-CoV-2 genomic sequences of high quality from GISAID were analyzed and a network of the common mutations of the lineages was constructed. The conserved unique mutations specific for SARS-CoV-2 VOCs were found. Then, ARMS-RT-qPCR assays based on the two unique mutations of the Alpha and Delta variants were developed for the detection of the two VOCs. Application of the assay in clinical samples demonstrated that the current method is a convenient, cost-effective, and rapid way to screen the target SARS-CoV-2 VOCs.