Joint-GWAS, Linkage Mapping, and Transcriptome Analysis to Reveal the Genetic Basis of Plant Architecture-Related Traits in Maize.

Plant architecture is one of the key factors affecting maize yield formation and can be divided into secondary traits, such as plant height (PH), ear height (EH), and leaf number (LN). It is a viable approach for exploiting genetic resources to improve plant density. In this study, one natural panel of 226 inbred lines and 150 family lines derived from the offspring of T32 crossed with Qi319 were genotyped by using the MaizeSNP50 chip and the genotyping by sequence (GBS) method and phenotyped under three different environments. Based on the results, a genome-wide association study (GWAS) and linkage mapping were analyzed by using the MLM and ICIM models, respectively. The results showed that 120 QTNs (quantitative trait nucleotides) and 32 QTL (quantitative trait loci) related to plant architecture were identified, including four QTL and 40 QTNs of PH, eight QTL and 41 QTNs of EH, and 20 QTL and 39 QTNs of LN. One dominant QTL, qLN7-2, was identified in the Zhangye environment. Six QTNs were commonly identified to be related to PH, EH, and LN in different environments. The candidate gene analysis revealed that Zm00001d021574 was involved in regulating plant architecture traits through the autophagy pathway, and Zm00001d044730 was predicted to interact with the male sterility-related gene ms26. These results provide abundant genetic resources for improving maize plant architecture traits by using approaches to biological breeding.

Iron chelation prevents nigrostriatal neurodegeneration in a chronic methamphetamine mice model.

Methamphetamine (METH) has been established to selectively target and impair dopaminergic neurons through multiple pathways. Ferroptosis is a unique form of non-apoptotic cell death driven by cellular iron accumulation-induced lipid peroxidation. Nonetheless, it remains unclear whether METH can induce ferroptosis. In the present study, we sought to assess alterations in iron levels after chronic METH exposure and reveal the modulatory role of iron on METH-induced pathologies. Importantly, we demonstrated that METH increased iron deposition in the nigrostriatal system, including the substantia nigra (SN) and caudate putamen (CPu). Moreover, decreases in GPx4 levels, increases in lipid peroxidation products, and pathological alterations were observed in the nigrostriatal system as a consequence of chronic METH exposure. The iron chelator deferiprone not only alleviated nigrostriatal iron deposition, dopaminergic cell death, and lipid peroxidation, but alsoattenuated the decreases in GPx4 induced by METH. These findings suggest an alleviation of ferroptosis in dopaminergic neurons. In addition, we found that the ferroptosis inhibitor liproxstatin-1 attenuated METH-induced dopaminergic degeneration in the nigrostriatal system. Our findings corroborated that METH might induce dopaminergic neurodegeneration through iron-dependent ferroptosis. Interestingly, reducing iron levels or inhibiting ferroptosis may alleviate METH-induced dopaminergic neurodegeneration.

Whole genome sequence of carbapenem-resistant hypermucoviscous Klebsiella pneumoniae K2-ST375 with blaNDM-harbouring conjugative IncX3 and pLVPK-like virulence plasmids from a patient in China.

OBJECTIVES: Carbapenem-resistant hypermucoviscous Klebsiella pneumoniae (CR-HMKP) poses unprecedented public health challenges. However, genomic information regarding the CR-HMKP K2-ST375 strain is scarce. The aim of this study was to characterize the whole genome sequence of the CR-HMKP K2-ST375 strain Kp0179 isolated from a male patient in China. METHODS: The whole genome of Kp0179 was sequenced using the DNBSEQ and Pacific Biosciences RSII platforms. The capsular serotype, multilocus sequence typing (MLST), antimicrobial resistance genes, and virulence factors were determined using available databases and bioinformatics tools. Conjugation experiments were performed using rifampicin-resistant Escherichia coli C600 as the recipient. RESULTS: The Kp0179 strain with hypermucoviscous phenotype was resistant to almost all ß-lactams, including ertapenem and imipenem. Whole genome sequencing revealed that Kp0179 belonged to K2-ST375 and contained blaNDM-IncX3 and a virulence plasmid ca. 121 kb. Kp0179 contained 5146 coding genes, 88 tRNAs, 25 rRNAs and 38 non-coding RNA genes. Among the six acquired antibiotic resistance genes, blaSHV-99, fosA, oqxAB were located on the chromosome, whereas blaNDM-1, qnrS1 and blaSHV-12 were located on the conjugative plasmid pNDM-Kp0179 (IncX3 type). Virulence gene analysis indicated that pLVPK-Kp0179 carried multiple virulence-encoding genes, such as iroBCDN, iucABCDiutA, rmpA and rmpA2. In addition to carrying a virulence plasmid, capsule formation (kvgA) and the type 3 fimbriae operon (mrkABCDFHIJ) were located on the chromosome of Kp0179. CONCLUSION: To our knowledge, this is the first report of a CR-HMKP K2-ST375 strain with a blaNDM-harboured conjugative IncX3 plasmid and a pLVPK-like virulence plasmid from a patient in China. Therefore, the spread of CR-HMKP K2-ST375 isolates in China should be closely monitored.

Deep Learning-Based Non-Contact IPPG Signal Blood Pressure Measurement Research.

In this paper, a multi-stage deep learning blood pressure prediction model based on imaging photoplethysmography (IPPG) signals is proposed to achieve accurate and convenient monitoring of human blood pressure. A camera-based non-contact human IPPG signal acquisition system is designed. The system can perform experimental acquisition under ambient light, effectively reducing the cost of non-contact pulse wave signal acquisition while simplifying the operation process. The first open-source dataset IPPG-BP for IPPG signal and blood pressure data is constructed by this system, and a multi-stage blood pressure estimation model combining a convolutional neural network and bidirectional gated recurrent neural network is designed. The results of the model conform to both BHS and AAMI international standards. Compared with other blood pressure estimation methods, the multi-stage model automatically extracts features through a deep learning network and combines different morphological features of diastolic and systolic waveforms, which reduces the workload while improving accuracy.

Integrated IBD Analysis, GWAS Analysis and Transcriptome Analysis to Identify the Candidate Genes for White Spot Disease in Maize.

Foundation parents (FPs) play an irreplaceable role in maize breeding practices. Maize white spot (MWS) is an important disease in Southwest China that always seriously reduces production. However, knowledge about the genetic mechanism of MWS resistance is limited. In this paper, a panel of 143 elite lines were collected and genotyped by using the MaizeSNP50 chip with approximately 60,000 single nucleotide polymorphisms (SNPs) and evaluated for resistance to MWS among 3 environments, and a genome-wide association study (GWAS) and transcriptome analysis were integrated to reveal the function of the identity-by-descent (IBD) segments for MWS. The results showed that (1) 225 IBD segments were identified only in the FP QB512, 192 were found only in the FP QR273 and 197 were found only in the FP HCL645. (2) The GWAS results showed that 15 common quantitative trait nucleotides (QTNs) were associated with MWS. Interestingly, SYN10137 and PZA00131.14 were in the IBD segments of QB512, and the SYN10137-PZA00131.14 region existed in more than 58% of QR273's descendants. (3) By integrating the GWAS and transcriptome analysis, Zm00001d031875 was found to located in the region of SYN10137-PZA00131.14. These results provide some new insights for the detection of MWS's genetic variation mechanisms.

The prospect of Xihuang pill in the treatment of cancers.

Background: Xihuang pill, a Traditional Chinese Medicine (TCM) prescription and a representative of Huoxuehuayu therapy (one of the TCM therapies to promote blood circulation and remove blood stasis), has been widely used in breast cancer treatments. Although some evidence suggests the efficacy and safety of the Xihuang pill in treating certain cancer, the overall efficacy of the Xihuang pill in other cancer treatment is uncertain. Objective: This study aimed to summarize the current clinical literature and provided evidence support for addressing the research question of whether the Xihuang pill is safe and effective in the treatment of various cancers as Huoxuehuayu therapy, and possibly identify the clinical dosage range and therapeutic effect of Xihuang pills. Method: Seven Chinese and English databases such as PubMed, CNKI, and Google Scholar were searched to collect the publications on Xihuang pill and cancer. Then the researchers extracted data from the articles that met the inclusion criteria and used SAS statistical program version 9.4 (by SAS Institute, Cary, North Carolina, USA) for statistical statistics. Results: Our search identified 78 studies, including 69 RCTs (randomized control trials), 6 NRCCs (non-randomized concurrent control trials), and 3 BAS (before-after study), evaluating 3151 patients in total. The daily doses of Xihuang pills/capsule were between 2 g and 60 g, and duration between 2 weeks and 5 years, mostly used in the middle or late stage of cancer. The therapeutic effect of the Xihuang pill was mainly reflected in improving Complete Response (CR, a term from The Response Evaluation Criteria In Solid Tumors) or Partial Response (PR, a term from The Response Evaluation Criteria In Solid Tumors), reducing adverse reactions, promoting quality of life (QoL), regulating immunity, alleviating pain, prolonging survival, reducing metastasis and recurrence, reducing inflammation, regulating estrogen levels, decreasing hypercoagulative status, and reducing tumor markers. Conclusion: Xihuang pill representing Huoxuehuayu therapy has a good prospect in the treatment of cancer.

Intelligent convolution neural network-assisted SERS to realize highly accurate identification of six pathogenic Vibrio.

Based on label-free SERS technology, the relationship between the Raman signals of pathogenic Vibrio microorganisms and purine metabolites was analyzed in detail. A deep learning CNN model was successfully developed, achieving a high accuracy rate of 99.7% in the identification of six typical pathogenic Vibrio species within 15 minutes, providing a new method for pathogen identification.

Integration of GWAS, linkage analysis and transcriptome analysis to reveal the genetic basis of flowering time-related traits in maize.

Maize (Zea mays) inbred lines vary greatly in flowering time, but the genetic basis of this variation is unknown. In this study, three maize flowering-related traits (DTT, days to tasselling; DTP, days to pollen shed; DTS, days to silking) were evaluated with an association panel consisting of 226 maize inbred lines and an F2:3 population with 120 offspring from a cross between the T32 and Qi319 lines in different environments. A total of 82 significant single nucleotide polymorphisms (SNPs) and 117 candidate genes were identified by genome-wide association analysis. Twenty-one quantitative trait loci (QTLs) and 65 candidate genes were found for maize flowering time by linkage analysis with the constructed high-density genetic map. Transcriptome analysis was performed for Qi319, which is an early-maturing inbred line, and T32, which is a late-maturing inbred line, in two different environments. Compared with T32, Qi319 showed upregulation of 3815 genes and downregulation of 3906 genes. By integrating a genome-wide association study (GWAS), linkage analysis and transcriptome analysis, 25 important candidate genes for maize flowering time were identified. Together, our results provide an important resource and a foundation for an enhanced understanding of flowering time in maize.

Dynamic patterns of gene expression and regulatory variation in the maize seed coat.

BACKGROUND: Seed size is an important factor contributing to maize yield, but its molecular mechanism remains unclear. The seed coat, which serves as one of the three components of the maize grain, determines seed size to a certain extent. The seed coat also shares the maternal genotype and is an ideal material for studying heterosis. RESULTS: In this study, the self-pollinated seeds of the maize hybrid Yudan888 and its parental lines were continuously collected from 0 day after pollination (DAP) to 15 DAP for phenotyping, cytological observation and RNA-seq. The phenotypic data showed that 3 DAP and 8 DAP are the best time points to study maize seed coat heterosis. Cytological observations indicated that maize seed coat heterosis might be the result of the coordination between cell number and cell size. Furthermore, the RNA-seq results showed that the nonadditive genes changed significantly between 3 and 8 DAP. However, the number of genes expressed additively was not significantly different. Our findings suggest that seed coat heterosis in hybrid is the result of nonadditive expression caused by dynamic changes in genes at different time points during seed expansion and seed coat development. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that genes related to DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation contributed significantly to hybrid seed coat heterosis. CONCLUSION: Maize seed coat phenotyping allowed us to infer that 3 DAP and 8 DAP are important time points in the study of seed coat heterosis. Our findings provide evidence for genes involved in DNA replication, cell cycle regulation, circadian rhythms and metabolite accumulation in hybrid with high or low parental expression as major contributors to hybrid seed coat heterosis.

Immune therapy: a new therapy for acute myeloid leukemia.

Although complete remission could be achieved in about 60%-70% of acute myeloid leukemia (AML) patients after conventional chemotherapy, relapse and the state of being refractory to treatment remain the main cause of death. In addition, there is a great need for less intensive regimens for all medically frail patients (both due to age/comorbidity and treatment-related). Immune therapy anticipates improved prognosis and reduced toxicities, which may offer novel therapeutic rationales. However, one of the major difficulties in developing immune therapies against AML is that the target antigens are also significantly expressed on healthy hematopoietic stem cells; B-cell malignancies are different because CD20/CD19/healthy B-cells are readily replaceable. Only the anti-CD33 antibody-drug conjugate gemtuzumab-ozogamicin is approved by the FDA for AML. Thus, drug development remains extremely active, although it is still in its infancy. This review summarizes the clinical results of immune therapeutic agents for AML, such as antibody-based drugs, chimeric antigen receptor therapy, checkpoint inhibitors, and vaccines.

Emerging Omicron subvariants evade neutralizing immunity elicited by vaccine or BA.1/BA.2 infection.

The newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2.75 and BA.2.76 subvariants contained 35 and 29 additional mutations in its spike (S) protein compared with the reference SARS-CoV-2 genome, respectively. Here, we measured the evasion degree of the BA.1, BA.2, BA.4, BA.5, BA.2.75, and BA.2.76 subvariants from neutralizing immunity in people previously infected with the Omicron BA.1 and BA.2, determined the effect of vaccination on immune evasion, and compared the titers of neutralizing antibodies in serums between acute infection and convalescence. Results showed that the neutralization effect of serums from patients with different vaccination statuses and BA.1/BA.2 breakthrough infection decreased with the Omicron evolution from BA.1 to BA.2, BA.4, BA.5, BA.2.75, and BA.2.76. This study also indicated that the existing vaccines could no longer provide effective protection, especially for the emerging BA.2.75 and BA.2.76 subvariants. Therefore, vaccines against emerging epidemic strains should be designed specifically. In the future, we can not only focus on the current strains, but also predict and design new vaccines against potential mutant strains. At the same time, we can combine the virus strains' infection characteristics to develop protective measures for virus colonization areas, such as nasal protection spray. Besides, further studies on the Y248N mutation of BA.2.76 subvariant were also necessary to explore its contribution to the enhanced immune evasion ability.

Evidence for human infection with avian influenza A(H9N2) virus via environmental transmission inside live poultry market in Xiamen, China.

H9N2 avian influenza virus (AIV) has become prevalent in the live poultry market (LPM) worldwide, and environmental transmission mode is an important way for AIVs to infect human beings in the LPM. To find evidence of human infection with the influenza A(H9N2) virus via environmental contamination, we evaluated one human isolate and three environmental isolates inside LPMs in Xiamen, China. The phylogeny, transmissibility, and pathogenicity of the four isolates were sorted out systematically. As for the H9N2 virus, which evolved alongside the "Avian-Environment-Human" spreading chain in LPMs from the summer of 2019 to the summer of 2020, its overall efficiency of contact and aerosol transmissibility improved, which might contribute to the increasing probability of human infection. This study indicated that environmental exposure might act as an important source of human infection in LPMs.

An integrated interval-valued intuitionistic fuzzy technique for resumption risk assessment amid COVID-19 prevention.

Currently, China has achieved a remarkable achievement on the containment of COVID-19, which creates a favorable condition for the gradual resumption of normal life. However, COVID-19 infections continue to rise in many nations and some sporadic cases occur from time to time in China, which still poses some risks to the resumption. Hence, it is imperative to develop some reasonable techniques to assess the resumption risk. This paper aims to investigate an integrated interval-valued intuitionistic fuzzy (IVIF) technique to adroitly assess the resumption risk based on DEMATEL (decision making trial and evaluation laboratory), BWM (best-worst method) and SPA (set pair analysis). This integrated technique is called IVIF-DBWM-SPA, where the IVIF-DBWM (combined by the IVIF-DEMATEL and IVIF-BWM) is used to determine the global criteria weights and the IVIF-SPA is employed to generate the ranking order of the alternatives. The IVIF-DEMATEL and IVIF-BWM are used to determine the weights of dimensions and the weights of criteria under each dimension, respectively. In this IVIF-BWM, two bi-objective programming models are constructed by regarding experts' pessimistic and optimistic attitudes, respectively. Combined experts' intrapersonal and interpersonal uncertainties simultaneously, a bi-objective programming model is proposed to derive the dynamic weights of experts. Based on the determined weights of experts and criteria, an IVIF-SPA is developed to assess the risk levels of all alternatives. The validity of the proposed technique is demonstrated with a real case of college resumption risk assessment amid COVID-19. Some sensitivity and comparison analyses are provided to show the merits of the proposed technique.

Knockdown of let-7b in leukemia associated macrophages inhibit acute myeloid leukemia progression.

Macrophages, critical components of bone marrow microenvironment, are reported to be remodeled into leukemia-associated macrophages (LAMs) in leukemic microenvironment where they contribute to leukemia development, characterized as M2 macrophages with pro-tumor effects. However, how leukemic microenvironment transforms macrophages into LAMs remains unknown. Here, we analyzed the clinical relevance of LAMs and profiled their RNA-Seq from acute myeloid leukemia (AML) patients with complete remission (CR) after induction treatment and refractory AML patients. Our results showed that the proportion and number of LAMs in refractory AML patients was higher than that in CR patients and LAM was a poor prognostic factor of AML patients. Furthermore, let-7b was a potentially aberrant gene in LAMs contributed to M2-subtype characteristics. Knockdown of let-7b in LAMs could inhibit the development of AML by repolarizing LAMs toward M1-subtype characteristics through the activation of Toll-like receptor and NF-κB pathway. Our study provides insight for future LAM-based immunotherapy strategies for AML.

Over expression of ubiquitin-conjugating enzyme E2O in bone marrow mesenchymal stromal cells partially attenuates acute myeloid leukaemia progression.

Bone marrow mesenchymal stromal cells (BM-MSCs) are implicated in the pathogenesis of acute myeloid leukaemia (AML). However, due to the high heterogeneity of AML the mechanism underlying the cross-talk between MSCs and leukaemia cells is not well understood. We found that mixed-lineage leukaemia-AF9 (MLL-AF9)-induced AML mice-derived MSCs had higher proliferative viability compared to wild-type mice-derived MSCs with ubiquitin-conjugating enzyme E2O (Ube2o) down-regulation. After overexpression of UBE2O in AML-derived MSCs, the growth capacity of MSCs was reduced with nuclear factor kappa B subunit 1 (NF-κB) pathway deactivation. In vitro co-culture assay revealed that UBE2O-overexpression MSCs suppressed the proliferation and promoted apoptosis of AML cells by direct contact. In vivo results revealed that the leukaemia burden was reduced and the overall survival of AML mice was prolonged, with decreased dissemination of leukaemia cells in BM, spleen, liver and peripheral blood. Additionally, subcutaneous tumorigenesis revealed that tumour growth was also suppressed in the UBE2O-overexpression MSCs group. In conclusion, UBE2O was expressed at a low level in MLL-AF9-induced AML mice-derived MSCs. Overexpression of UBE2O in MSCs suppressed their proliferation through NF-κB pathway deactivation, which resulted in AML suppression. Our study provides a theoretical basis for a BM microenvironment-based therapeutic strategy to control disease progression.

Etiologic characteristics of avian influenza H11 viruses isolated from the live poultry market in southeast coastal region in China.

Since it was first identified in 1956, the H11 subvariant influenza virus has been reported worldwide. However, due to the low pathogenicity of the H11 subvariant and the absence of its widespread transmission among humans, there are only a few reports on the etiology of the H11 subvariant influenza virus. Therefore, in the present study, we isolated a strain of the H11N3 avian influenza virus (AIV) from poultry feces from the live poultry market in the southeast coastal region of China. Considering that the H11 subvariant is known to cause infections in humans and to enrich the knowledge of the H11 subvariant of the avian influenza virus, the genetics, pathogenicity, and transmissibility of the isolate were studied. The phylogenetic analysis indicated that the H11N3 isolate was of Eurasian origin and carried genes closely related to duck H7N2 and H4N6. The receptor binding analysis revealed that the H11N3 isolate only acquired a binding affinity for avian-derived receptors. In the respiratory system of mice, the isolate could directly cause infection without adaptation. In addition, the results from transmission experiments and antibody detection in guinea pigs demonstrated that H11N3 influenza viruses can efficiently transmit through the respiratory tract in mammalian models. Direct infection of the H11N3 influenza virus without adaptation in the mouse models and aerosol transmission between guinea pig models confirms its pandemic potential in mammals, underscoring the importance of monitoring rare influenza virus subtypes in future studies.

A study on the evolution of economic patterns and urban network system in Guangdong-Hong Kong-Macao greater bay area.

The COVID-19 pandemic has seriously affected China's macroeconomy, industrial transformation, and high-quality development. Research on economic patterns and urban network systems can provide a reference for healthy development of the regional economic system. The evolution of the economic pattern and urban network system of Guangdong-Hong Kong-Macao Greater Bay Area (GBA) from 2010 to 2020 is investigated using methods (e.g., the gravity center model, the gravitational force model, social network analysis, and geographic information system). (1) The gravity center of gross domestic product (GDP) of the GBA is located in Nansha district, Guangzhou, with a skewing direction northwest-east-northwest and a movement rate of "large-small-large." The center of import and export and the center of consumption show a "zigzagging migration" in which the center of investment shows an "irregular (random) migration". (2) The economic connection degree of cities in the GBA exhibits a high ascending velocity, and the whole area tends to be mature, with a significant effect of spatial proximity. With the steady increase in network density, there is significant polarization of network centrality in the region. The four major cohesive subgroups have been relatively stable and consistent with the degree of geographic proximity of the cities. The center-periphery structure is more significant, in which the core area is extended to the cities on the east coast of the Pearl River Estuary, thus forming the core cluster of "Hong Kong-Shenzhen-Guangzhou-Dongguan." In this study, the evolution of economic patterns and urban network systems in the GBA over the past decade is analyzed using multiple methods (i.e., gravity model, urban network system analysis, and geographic information system) based on urban socioeconomic data by starting from various spatial elements (e.g., "points, lines, and networks") to gain insights into and optimize research on regional economic development after the COVID-19 pandemic.

A retrospective analysis of EBV-DNA status with the prognosis of lymphoma.

Epstein-Barr virus (EBV) infection is proved to be associated with clinicopathology of lymphoma. However, little is known about the relationship between EBV-DNA status after treatment and prognosis. In this study, real-time polymerase chain reaction (PCR) was used for quantitative detection of EBV-DNA load in peripheral blood of all 26,527 patients with lymphoma, and the clinical characteristics and prognosis of 202 patients were retrospectively analysed, including 100 patients with positive EBV-DNA and 102 randomly selected patients with negative EBV-DNA. We found that the average rate of EBV-DNA positivity in lymphomas was 0.376%, and EBV-DNA-positive patients presented higher risk with elevated lactate dehydrogenase (LDH) and ß2-MG level, B symptoms, secondary hemophagocytic syndrome and lower objective response rate compared to EBV-DNA-negative patients. Multivariate analysis revealed EBV-DNA-positive patients had inferior progression-free survival (PFS) and overall survival (OS) and EBV-DNA level before treatment was related to PFS but not OS of T/NK cell lymphoma. In T/NK cell lymphoma, EBV-DNA converting negative after treatment was correlated with better PFS but not OS, and second-line therapy could induce more EBV-DNA-negative conversion compared to CHOP-based therapy. In all, EBV-DNA positivity before treatment can be a biomarker representing the tumour burden and an independent prognostic factor. EBV-DNA-negative conversion after treatment is a good prognostic factor for T/NK cell lymphomas.

Accessible and Adaptable Multiplexed Real-Time PCR Approaches to Identify SARS-CoV-2 Variants of Concern.

Rapid identification and continuous surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are critical for guiding the response to the COVID-19 pandemic. Whole-genome sequencing (WGS) is a preferred tool for this aim, but many laboratories suffer from a lack of resources to support population-level sequencing. Here, we describe two PCR strategies targeting spike protein mutations to identify the Alpha, Delta, and Omicron variants. Signature mutations were selected using a dedicated bioinformatic program. The selected mutations in Alpha and Delta variants were detected using multicolor melting curve analysis (MMCA). Thirty-two mutations of the Omicron variant were targeted using the MeltArray approach in one reaction, which was able to detect the Omicron subvariants BA.1, BA.2, BA.3, and BA.4/5. The limits of detection varied from five to 50 copies of RNA templates/reactions. No cross-reactivity was observed with nine other respiratory viruses, including other coronaviruses. We validated the MMCA and MeltArray assays using 309 SARS-CoV-2 positive samples collected at different time points. These assays exhibited 98.3% to 100% sensitivity and 100% specificity compared with WGS. Multiplexed real-time PCR strategies represent an alternative tool capable of identifying current SARS-CoV-2 VOCs, adaptable for emerging variants and accessible for laboratories using existing equipment and personnel. IMPORTANCE Rapid detection and mutation surveillance of SARS-CoV-2 VOCs is crucial for COVID-19 control, management, and prevention. We developed two rapid molecular assays based on the real-time PCR platform to identify important variants of concern, including the Omicron variant with a large number of mutations. Signature mutations were selected by an R program. Then, MMCA assays were established for Alpha and Delta variants, and a MeltArray assay targeting 32 mutations was developed for Omicron variant. These multiplexed PCR assays could be performed in a 96-well real-time PCR instrument within 2.5 h, offering a high-throughput choice for dynamic monitoring of SARS-CoV-2 VOCs in a standard microbiology laboratory.