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For: Gruca A, Ziemska-Legiecka J, Jarnot P, Sarnowska E, Sarnowski TJ, Grynberg M. Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development. BMC Bioinformatics 2021;22:182. [PMID: 33832440 PMCID: PMC8027979 DOI: 10.1186/s12859-021-04017-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open

For:	Gruca A, Ziemska-Legiecka J, Jarnot P, Sarnowska E, Sarnowski TJ, Grynberg M. Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development. BMC Bioinformatics 2021;22:182. [PMID: 33832440 PMCID: PMC8027979 DOI: 10.1186/s12859-021-04017-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open

Number

Cited by Other Article(s)

Yang CR, Chang SY, Gong YN, Huang CG, Tung TH, Liu W, Chan TC, Hung KS, Shang HS, Tsai JJ, Kao CL, Wu HL, Daisy Liu LY, Lin WY, Fan YC, King CC, Ku CC. The emergence and successful elimination of SARS-CoV-2 dominant strains with increasing epidemic potential in Taiwan's 2021 outbreak. Heliyon 2023;9:e22436. [PMID: 38107297 PMCID: PMC10724543 DOI: 10.1016/j.heliyon.2023.e22436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open

Abstract

Taiwan's experience with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 guided its development of strategies to defend against SARS-CoV-2 in 2020, which enabled the successful control of Coronavirus disease 2019 (COVID-19) cases from 2020 through March 2021. However, in late-April 2021, the imported Alpha variant began to cause COVID-19 outbreaks at an exceptional rate in Taiwan. In this study, we aimed to determine what epidemiological conditions enabled the SARS-CoV-2 Alpha variant strains to become dominant and decline later during a surge in the outbreak. In conjunction with contact-tracing investigations, we used our bioinformatics software, CoVConvert and IniCoV, to analyze whole-genome sequences of 101 Taiwan Alpha strains. Univariate and multivariable regression analyses revealed the epidemiological factors associated with viral dominance. Univariate analysis showed the dominant Alpha strains were preferentially selected in the surge's epicenter (p = 0.0024) through intensive human-to-human contact and maintained their dominance for 1.5 months until the Zero-COVID Policy was implemented. Multivariable regression found that the epidemic periods (p = 0.007) and epicenter (p = 0.001) were two significant factors associated with the dominant virus strains spread in the community. These dominant virus strains emerged at the outbreak's epicenter with frequent human-to-human contact and low vaccination coverage. The Level 3 Restrictions and Zero-COVID policy successfully controlled the outbreak in the community without city lockdowns. Our integrated method can identify the epidemiological conditions for emerging dominant virus with increasing epidemiological potential and support decision makers in rapidly containing outbreaks using public health measures that target fast-spreading virus strains.

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Affiliation(s)

Chin-Rur Yang Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC
Sui-Yuan Chang Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC Dept. of Laboratory Medicine, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC
Yu-Nong Gong Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC
Chung-Guei Huang Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC Dept. of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC
Tsung-Hua Tung Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC Dept. of Health, Taipei City Government, Taipei, Taiwan, ROC
Wei Liu Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
Ta-Chien Chan Research Center for Humanities and Social Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC
Kuo-Sheng Hung Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC
Hung-Sheng Shang Division of Clinical Pathology, Dept. of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC
Jih-Jin Tsai School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC
Chuan-Liang Kao Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
Hui-Lin Wu Hepatitis Research Center, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
Li-Yu Daisy Liu Division of Biometry, Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan, ROC
Wan-Yu Lin Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
Yi-Chin Fan Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
Chwan-Chuen King Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
Chia-Chi Ku Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC

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Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS. Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils. Nat Commun 2023;14:2379. [PMID: 37185252 PMCID: PMC10127185 DOI: 10.1038/s41467-023-37865-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open

Affiliation(s)

Einav Tayeb-Fligelman Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Jeannette T Bowler Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Christen E Tai Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
Michael R Sawaya Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
Yi Xiao Jiang Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Gustavo Garcia Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
Sarah L Griner Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Xinyi Cheng Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Lukasz Salwinski Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
Liisa Lutter Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Paul M Seidler Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Pharmacology and Pharmaceutical Sciences, University of Southern California School of Pharmacy, Los Angeles, CA, 90089-9121, USA
Jiahui Lu Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Gregory M Rosenberg Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Ke Hou Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Romany Abskharon Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Hope Pan Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Chih-Te Zee Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
David R Boyer Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Yan Li Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
Daniel H Anderson Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Kevin A Murray Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
Genesis Falcon UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
Duilio Cascio UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
Lorena Saelices Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
Robert Damoiseaux Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA Department of Bioengineering, UCLA, Los Angeles, CA, 90095, USA California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
Vaithilingaraja Arumugaswami Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
Feng Guo Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
David S Eisenberg Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA. Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA. Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA. Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA. UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA. California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.

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Markarian NM, Galli G, Patel D, Hemmings M, Nagpal P, Berghuis AM, Abrahamyan L, Vidal SM. Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency. Front Microbiol 2022;13:933983. [PMID: 35847101 PMCID: PMC9283111 DOI: 10.3389/fmicb.2022.933983] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open

Pashova S, Balabanski L, Elmadjian G, Savov A, Stoyanova E, Shivarov V, Petrov P, Pashov A. Restriction of the Global IgM Repertoire in Antiphospholipid Syndrome. Front Immunol 2022;13:865232. [PMID: 35493489 PMCID: PMC9043687 DOI: 10.3389/fimmu.2022.865232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open

Abstract

The typical anti-phospholipid antibodies (APLA) in the anti-phospholipid syndrome (APS) are reactive with the phospholipid-binding protein β2GPI as well as a growing list of other protein targets. The relation of APLA to natural antibodies and the fuzzy set of autoantigens involved provoked us to study the changes in the IgM repertoire in APS. To this end, peptides selected by serum IgM from a 7-residue linear peptide phage display library (PDL) were deep sequenced. The analysis was aided by a novel formal representation of the Igome (the mimotope set reflecting the IgM specificities) in the form of a sequence graph. The study involved women with APLA and habitual abortions (n=24) compared to age-matched clinically healthy pregnant women (n=20). Their pooled Igomes (297 028 mimotope sequences) were compared also to the global public repertoire Igome of pooled donor plasma IgM (n=2 796 484) and a set of 7-mer sequences found in the J regions of human immunoglobulins (n=4 433 252). The pooled Igome was represented as a graph connecting the sequences as similar as the mimotopes of the same monoclonal antibody. The criterion was based on previously published data. In the resulting graph, identifiable clusters of vertices were considered related to the footprints of overlapping antibody cross-reactivities. A subgraph based on the clusters with a significant differential expression of APS patients’ mimotopes contained predominantly specificities underrepresented in APS. The differentially expressed IgM footprints showed also an increased cross-reactivity with immunoglobulin J regions. The specificities underexpressed in APS had a higher correlation with public specificities than those overexpressed. The APS associated specificities were strongly related also to the human peptidome with 1 072 mimotope sequences found in 7 519 human proteins. These regions were characterized by low complexity. Thus, the IgM repertoire of the APS patients was found to be characterized by a significant reduction of certain public specificities found in the healthy controls with targets representing low complexity linear self-epitopes homologous to human antibody J regions.

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Becerra A, Muñoz-Velasco I, Aguilar-Cámara A, Cottom-Salas W, Cruz-González A, Vázquez-Salazar A, Hernández-Morales R, Jácome R, Campillo-Balderas JA, Lazcano A. Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein. Sci Rep 2022;12:936. [PMID: 35042962 PMCID: PMC8766472 DOI: 10.1038/s41598-022-04976-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/04/2022] [Indexed: 11/24/2022] Open

Lobiuc A, Dimian M, Gheorghita R, Sturdza OAC, Covasa M. Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Front Microbiol 2021;12:654417. [PMID: 34305826 PMCID: PMC8292954 DOI: 10.3389/fmicb.2021.654417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/14/2021] [Indexed: 12/23/2022] Open

Abstract

Romania officially declared its first Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) case on February 26, 2020. The first and largest coronavirus disease 2019 (COVID-19) outbreak in Romania was recorded in Suceava, North-East region of the country, and originated at the Suceava regional county hospital. Following sheltering-in-place measures, infection rates decreased, only to rise again after relaxation of measures. This study describes the spread of SARS-CoV-2 in Suceava and other parts of Romania and analyses the mutations and their association with clinical manifestation of the disease during the period of COVID-19 outbreak. Sixty-two samples were sequenced via high-throughput platform and screened for variants. For selected mutations, putative biological significance was assessed, and their effects on disease severity. Phylogenetic analysis was conducted on Romanian genomes (n = 112) and on sequences originating from Europe, United Kingdom, Africa, Asia, South, and North America (n = 876). The results indicated multiple introduction events for SARS-CoV-2 in Suceava, mainly from Italy, Spain, United Kingdom, and Russia although some sequences were also related to those from the Czechia, Belgium, and France. Most Suceava genomes contained mutations common to European lineages, such as A20268G, however, approximately 10% of samples were missing such mutations, indicating a possible different arrival route. While overall genome regions ORF1ab, S, and ORF7 were subject to most mutations, several recurring mutations such as A105V were identified, and these were mainly present in severe forms of the disease. Non-synonymous mutations, such as T987N (Thr987Asn in NSP3a domain), associated with changes in a protein responsible for decreasing viral tethering in human host were also present. Patients with diabetes and hypertension exhibited higher risk ratios (RR) of acquiring severe forms of the disease and these were mainly related to A105V mutation. This study identified the arrival routes of SARS-CoV-2 in Romania and revealed potential associations between the SARS-CoV-2 genomic organization circulating in the country and the clinical manifestation of COVID-19 disease.

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