Towards precision medicine: Omics approach for COVID-19 DOI Creative Commons
Xiaoping Cen,

Feng-ao Wang,

Xinhe Huang

et al.

Biosafety and Health, Journal Year: 2023, Volume and Issue: 5(2), P. 78 - 88

Published: Jan. 18, 2023

The coronavirus disease 2019 (COVID-19) pandemic had a devastating impact on human society. Beginning with genome surveillance of severe acute respiratory syndrome 2 (SARS-CoV-2), the development omics technologies brought clearer understanding complex SARS-CoV-2 and COVID-19. Here, we reviewed how omics, including genomics, proteomics, single-cell multi-omics, clinical phenomics, play roles in answering biological questions about Large-scale sequencing advanced analysis methods facilitate COVID-19 discovery from virus evolution severity risk prediction to potential treatment identification. Omics would indicate precise globalized prevention medicine for under utilization big data capability phenotypes refinement. Furthermore, decoding rule by deep learning models is promising forecast new variants achieve more predict future pandemics prevent them time.

Language: Английский

Next-generation sequencing of host genetics risk factors associated with COVID-19 severity and long-COVID in Colombian population DOI Creative Commons
Mariana Angulo-Aguado, Juan Camilo Carrillo-Martínez,

Nora Constanza Contreras-Bravo

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 11, 2024

Abstract Coronavirus disease 2019 (COVID-19) was considered a major public health burden worldwide. Multiple studies have shown that susceptibility to severe infections and the development of long-term symptoms is significantly influenced by viral host factors. These findings highlighted potential genetic markers identify high-risk individuals develop target interventions reduce morbimortality. Despite its importance, factors remain largely understudied in Latin-American populations. Using case–control design custom next-generation sequencing (NGS) panel encompassing 81 variants 74 genes previously associated with COVID-19 severity long-COVID, we analyzed 56 asymptomatic or mild critical cases. In agreement previous studies, our results support association between several clinical variables, including male sex, obesity common like cough dyspnea, COVID-19. Remarkably, thirteen showed an severity. Among these variants, rs11385942 ( p < 0.01; OR = 10.88; 95% CI 1.36–86.51) located LZTFL1 gene, rs35775079 0.02; 8.53; 1.05–69.45) CCR3 strongest associations. Various respiratory systemic symptoms, along rs8178521 variant 2.51; 1.27–4.94) IL10RB were presence long-COVID. The predictive model comparison mixed model, which incorporates non-genetic outperforms models. To knowledge, this first study Colombia Latin-America proposing for long-COVID based on genomic analysis. Our highlights usefulness approaches studying risk specific methodology used allowed us validate Finally, integrated illustrates importance considering precision medicine infectious diseases.

Language: Английский

Citations

6
A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population DOI Creative Commons
Grace J. Kim, Jacob H. Elnaggar,

Mallory Varnado

et al.

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 15

Published: May 9, 2024

Long-term immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the identification of T-cell epitopes affecting host immunogenicity. In this computational study, we explored CD8 + epitope diversity estimated in 27 most common HLA-A and HLA-B alleles, representing United States population. Analysis 16 SARS-CoV-2 variants [B.1, Alpha (B.1.1.7), five Delta (AY.100, AY.25, AY.3, AY.3.1, AY.44), nine Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, XBB.1.5)] analyzed MHC class I alleles revealed that conservation was at 87.6%–96.5% spike (S), 92.5%–99.6% membrane (M), 94.6%–99% nucleocapsid (N). As virus mutated, an increasing proportion S experienced reduced predicted binding affinity: 70% BQ.1-XBB.1.5 decreased binding, as compared with ~3% ~15% earlier strains AY.100–AY.44 BA.1–BA.5, respectively. Additionally, identified several novel candidate HLA may be more susceptible to disease, notably HLA-A*32:01 , HLA-A*26:01 HLA-B*53:01 relatively protected from such HLA-A*31:01 HLA-B*40:01 HLA-B*44:03 HLA-B*57:01. Our findings support hypothesis viral genetic variation immunogenicity contributes determining clinical severity COVID-19. Achieving long-term COVID-19 will require understanding relationship between T cells, variants, genetics. This project is one first explore putatively impacts much

Language: Английский

Citations

6
In Silico Evaluation of Antifungal Compounds from Marine Sponges against COVID-19-Associated Mucormycosis DOI Creative Commons
Omkar Pokharkar,

Hariharan Lakshmanan,

Grigory V. Zyryanov

et al.

Marine Drugs, Journal Year: 2022, Volume and Issue: 20(3), P. 215 - 215

Published: March 20, 2022

The world is already facing the devastating effects of SARS-CoV-2 pandemic. A disseminated mucormycosis epidemic emerged to worsen this situation, causing havoc, especially in India. This research aimed perform a multitargeted docking study marine-sponge-origin bioactive compounds against mucormycosis. Information on proven drug targets and marine sponge was obtained via literature search. total seven different were selected. Thirty-five chosen using PASS online program. For homology modeling molecular docking, FASTA sequences 3D structures for protein retrieved from NCBI PDB databases. Autodock Vina PyRx 0.8 used studies. Further, dynamics simulations performed IMODS server top-ranked docked complexes. Moreover, drug-like properties toxicity analyses Lipinski parameters Swiss-ADME, OSIRIS, ProTox-II, pkCSM, StopTox servers. results indicated that naamine D, latrunculin S, (+)-curcudiol, (+)-curcuphenol, aurantoside I, hyrtimomine had highest binding affinity values -8.8, -8.6, -9.8, -11.4, -8.0, -9.0 kcal/mol, respectively. In sum, all MNPs included are good candidates (+)-curcudiol (+)-curcuphenol promising due their broad-spectrum target inhibition potential.

Language: Английский

Citations

27
SARS-CoV-2 and COVID-19: A Narrative Review DOI Creative Commons

Andrew D. Blann,

Rebekka Heitmar

British Journal of Biomedical Science, Journal Year: 2022, Volume and Issue: 79

Published: Sept. 6, 2022

The World Health Organisation has reported that the viral disease known as COVID-19, caused by SARS-CoV-2, is leading cause of death a single infectious agent. This narrative review examines certain components pandemic: its origins, early clinical data, global and UK-focussed epidemiology, vaccination, variants, long COVID.

Language: Английский

Citations

26
Exploring the possible molecular targeting mechanism of Saussurea involucrata in the treatment of COVID-19 based on bioinformatics and network pharmacology DOI
Dongdong Zhang, Zhaoye Wang, Jin Li

et al.

Computers in Biology and Medicine, Journal Year: 2022, Volume and Issue: 146, P. 105549 - 105549

Published: April 25, 2022

Language: Английский

Citations

25
SARS-CoV-2 infections and hospitalisations among immigrants in Norway-significance of occupation, household crowding, education, household income and medical risk: a nationwide register study DOI Creative Commons
Angela S. Labberton,

Anna Godøy,

Ingeborg Hess Elgersma

et al.

Scandinavian Journal of Public Health, Journal Year: 2022, Volume and Issue: 50(6), P. 772 - 781

Published: Feb. 14, 2022

As in other countries, the COVID-19 pandemic has affected Norway's immigrant population disproportionately, with significantly higher infection rates and hospitalisations. The reasons for this are uncertain.Through national emergency preparedness register, BeredtC19, we have studied laboratory-confirmed infections SARS-CoV-2 related hospitalisations entire Norwegian population, by birth-country background period 15 June 2020 to 31 March 2021, excluding first wave due limited test capacity restrictive criteria. Straightforward linkage of individual-level data allowed adjustment demographics, socioeconomic factors (occupation, household crowding, education income), underlying medical risk severe regression models.The sample comprised 5.49 million persons, which 0.91 were born outside Norway, there 82,532 confirmed cases 3088 Confirmed (per 100,000): foreign-born 3140, Norwegian-born parents 4799 parent(s) 1011. Hospitalisations 147, 47 37. addition base model (age, sex, municipality residence) attenuated excess 12.0% 3.8% among foreign-born, 10.9% 46.2%, respectively, foreign parents, compared parent(s).There large differences country background, these do not appear be fully explained factors. Our results may implications health policy, including targeting mitigation strategies.

Language: Английский

Citations

23
Post-Covid condition and clinic characteristics associated with SARS-CoV-2 infection: a 2-year follow-up to Brazilian cases DOI Creative Commons
Nayara Sousa da Silva, Nathália Kelly de Araújo, Katiusse Alves dos Santos

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Aug. 26, 2023

Until January 2023, Brazil recorded 37 million COVID-19 cases despite the decrease in mortality due to mass vaccination efforts against COVID-19. The infection continues challenge researchers and health professionals with persistent symptoms onset manifestations after acute phase of disease, namely Post-Covid Condition (PCC). Being one countries highest rate, must prepare for a growing number patients chronic consequences Longitudinal studies that follow over extended periods are crucial understanding long-term impacts COVID-19, including potential effects on quality life. We describe clinical profile cohort infected during first year pandemic follow-up two years investigate SARS-CoV-2 infection. wave featured extensive drug misuse, notably ineffective COVID kit comprised ivermectin, antimalarials azithromycin, elevated in-hospital mortality. In second study, was reported by symptomatic subjects across different severity levels Long haulers more likely be women, previously hospitalized, range from muscle pain cognitive deficit. Our longitudinal study is essential inform public authorities develop strategies policies control spread virus mitigate its society.

Language: Английский

Citations

14
The Immune Response of OAS1, IRF9, and IFI6 Genes in the Pathogenesis of COVID-19 DOI Open Access
Malena Gajate-Arenas, Ingrid Fricke-Galindo, Omar García-Pérez

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(9), P. 4632 - 4632

Published: April 24, 2024

COVID-19 is characterized by a wide range of clinical manifestations, where aging, underlying diseases, and genetic background are related to worse outcomes. In the present study, differential expression seven genes immunity,

Language: Английский

Citations

5
Genomic insight into COVID-19 severity in MAFLD patients: a single-center prospective cohort study DOI Creative Commons
Mykhailo Buchynskyi, Valentyn Oksenych, Iryna Kamyshna

et al.

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Sept. 4, 2024

This study investigated the influence of single nucleotide polymorphisms (SNPs) in genes associated with interferon pathway (IFNAR2 rs2236757), antiviral response (OAS1 rs10774671, OAS3 rs10735079), and viral entry (ACE2 rs2074192) on COVID-19 severity their association nonalcoholic fatty liver disease (MAFLD). We did not observe a significant between SNPs severity. While IFNAR2 rs2236757 A allele was correlated higher creatinine levels upon admission G lower band neutrophils discharge, these findings require further investigation. The distribution OAS gene (rs10774671 rs10735079) differ MAFLD patients non-MAFLD patients. Our population's ACE2 rs2074192 genotypes alleles differed from that European reference population. Overall, our suggest specific may be major contributors to patient population, highlighting potential role other genetic factors environmental influences.

Language: Английский

Citations

5
Current treatment strategies for COVID‑19 (Review) DOI Creative Commons
Fabin Han, Yanming Liu,

Mei Mo

et al.

Molecular Medicine Reports, Journal Year: 2021, Volume and Issue: 24(6)

Published: Oct. 15, 2021

The spread of the novel severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) emerged suddenly at end 2019 and disease came to be known as (COVID‑19). To date, there is no specific therapy established treat COVID‑19. Identifying effective treatments urgently required patients stop transmission SARS‑CoV‑2 in humans. For present review, >100 publications on therapeutic agents for COVID‑19, including

Language: Английский

Citations

29