Detection of SARS-CoV-2 Infection in Human Nasopharyngeal Samples by Combining MALDI-TOF MS and Artificial Intelligence

  1. García-Cuesta, Esteban
  2. Salvadó, Victoria
  3. Conde, José Elías 1
  4. Peña-Méndez, Eladia María 1
  5. Verdú, Enrique
  6. Boadas-Vaello, Pere
  7. Serrando, María Teresa
  8. Jiménez-Romero, Orlando
  9. Deulofeu, Meritxell
  1. 1 Universidad de La Laguna
    info

    Universidad de La Laguna

    San Cristobal de La Laguna, España

    GRID grid.10041.34

Journal:
Frontiers in Medicine

ISSN: 2296-858X

Year of publication: 2021

Volume: 8

Type: Article

Export: RIS
DOI: 10.3389/fmed.2021.661358 GOOGLE SCHOLAR

Metrics

Cited by

  • Scopus Cited by: 3 (04-12-2021)

JCR (Journal Impact Factor)

(Indicator corresponding to the last year available on this portal, year 2020)
  • Year 2020
  • Journal Impact Factor: 5.091
  • Best Quartile: Q1
  • Area: MEDICINE, GENERAL & INTERNAL Quartile: Q1 Rank in area: 28/167 (Ranking edition: SCIE)

SCImago Journal Rank

(Indicator corresponding to the last year available on this portal, year 2020)
  • Year 2020
  • SJR Journal Impact: 1.388
  • Best Quartile: Q1
  • Area: Medicine (miscellaneous) Quartile: Q1 Rank in area: 304/2448

CiteScore

(Indicator corresponding to the last year available on this portal, year 2020)
  • Year 2020
  • CiteScore of the Journal : 4.3
  • Area: Medicine (all) Percentile: 90

Journal Citation Indicator (JCI)

(Indicator corresponding to the last year available on this portal, year 2020)
  • Year 2020
  • Journal Citation Indicator (JCI): 1.09
  • Best Quartile: Q1
  • Area: MEDICINE, GENERAL & INTERNAL Quartile: Q1 Rank in area: 44/315

Abstract

The high infectivity of SARS-CoV-2 makes it essential to develop a rapid and accurate diagnostic test so that carriers can be isolated at an early stage. Viral RNA in nasopharyngeal samples by RT-PCR is currently considered the reference method although it is not recognized as a strong gold standard due to certain drawbacks. Here we develop a methodology combining the analysis of from human nasopharyngeal (NP) samples by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with the use of machine learning (ML). A total of 236 NP samples collected in two different viral transport media were analyzed with minimal sample preparation and the subsequent mass spectra data was used to build different ML models with two different techniques. The best model showed high performance in terms of accuracy, sensitivity and specificity, in all cases reaching values higher than 90%. Our results suggest that the analysis of NP samples by MALDI-TOF MS and ML is a simple, safe, fast and economic diagnostic test for COVID-19.

Bibliographic References

  • Coronavirus disease (COVID-2019) situation reports
  • Zaman, (2020), Preprints, 10.20944/preprints202005.0461.v1
  • Bai, (2020), JAMA., 323, pp. 1406, 10.1001/jama.2020.2565
  • Ji, (2020), Biosens Bioelectron., 166, pp. 112455, 10.1016/j.bios.2020.112455
  • Wu, (2020), Expert Rev Mol Diagn., 20, pp. 985, 10.1080/14737159.2020.1816171
  • Udugama, (2020), ACS Nano., 14, pp. 3822, 10.1021/acsnano.0c02624
  • Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases: interim guidance, 2 March 2020
  • Tahamtan, (2020), Expert Rev Mol Diagn., 20, pp. 453, 10.1080/14737159.2020.1757437
  • Williams, (2020), J Clin Microbiol., 58, pp. e00776-20, 10.1128/JCM.00776-20
  • Pasomsub, (2020), Clin Microbiol Infect., 27, pp. 285.e1, 10.1016/j.cmi.2020.05.001
  • Reeve, (2019), Biol Methods Protoc., 4, pp. bpz013, 10.1093/biomethods/bpz013
  • Welker, (2019), Expert Rev Proteomics., 16, pp. 695, 10.1080/14789450.2019.1645603
  • Majchrzykiewicz-Koehorst, (2015), J Virol Methods., 213, pp. 75, 10.1016/j.jviromet.2014.11.014
  • Calderaro, (2016), Sci Rep., 6, pp. 36082, 10.1038/srep36082
  • Deulofeu, (2019), Sci Rep., 9, pp. 7975, 10.1038/s41598-019-44215-1
  • Amato, (2013), J Appl Biomed., 11, pp. 47, 10.2478/v10136-012-0031-x
  • Marchetti-Deschmann, (2011), J Proteomics., 74, pp. 915, 10.1016/j.jprot.2011.04.024
  • Bäckryd, (2015), J Pain Res., 8, pp. 321, 10.2147/JPR.S82970
  • Sisignano, (2019), Pharmacol Ther, 199, pp. 16, 10.1016/j.pharmthera.2019.02.004
  • Nachtigall, (2020), Nat Biotechnol., 38, pp. 1168, 10.1038/s41587-020-0644-7
  • SoRelle, (2020), Clin Chem., 66, pp. 1367, 10.1093/clinchem/hvaa222
  • Friedman, (2001), Ann Stat., 29, pp. 1189, 10.1214/aos/1013203451
  • Boser, (1992), Proceedings of the fifth annual workshop on Computational learning theory (COLT '92), 10.1145/130385.130401
  • Albalat, (2013), Proteomics., 13, pp. 2967, 10.1002/pmic.201300100
  • Hossain, (2010), Electrospray and MALDI Mass Spectrometry. Fundamentals, Instrumentation, Practicalities, and Biological Applications, pp. 214
  • Chen, (2016), J Am Soc Mass Spectrom., 27, pp. 1227, 10.1007/s13361-016-1396-y
  • Harvey, (2013), Encyclopedia of Analytical Science, pp. 350
  • Zitek, (2020), West J Emerg Med., 21, pp. 470, 10.5811/westjem.2020.4.47370
  • Waller, (2020), AJR Am J Roentgenol., 215, pp. 834, 10.2214/AJR.20.23418
  • Lippi, (2020), Acta Biomed., 91, pp. 137, 10.23750/abm.v91i2.9548
  • Basso, (2020), Clin Chem Lab Med., 58, pp. 1579, 10.1515/cclm-2020-0749
  • Arevalo-Rodriguez, (2020), PLoS ONE., 15, pp. e0242958, 10.1371/journal.pone.0242958
  • Watson, (2020), BMJ., 369, pp. m1808, 10.1136/bmj.m1808
  • Feng, (2020), Anal Chem., 92, pp. 10196, 10.1021/acs.analchem.0c02060
  • Rogers, (2020), J Clin Microbiol., 58, pp. e00708, 10.1128/JCM.00708-20
  • Axell-House, (2020), J Infect., 81, pp. 681, 10.1016/j.jinf.2020.08.043
  • Shyu, (2020), Mo Med., 117, pp. 184
  • Tu, (2020), Crit Care Med., 48, pp. 1680, 10.1097/CCM.0000000000004594
  • Wang, (2020), Virus Res., 285, pp. 197988, 10.1016/j.virusres.2020.197988
  • Long, (2020), Eur J Radiol., 126, pp. 108961, 10.1016/j.ejrad.2020.108961
  • Bohn, (2020), Clin Chem Lab Med., 58, pp. 1037, 10.1515/cclm-2020-0722
  • Gao, (2020), J Microbiol Immunol Infect., 54, pp. 12, 10.1016/j.jmii.2020.05.001
  • Polack, (2020), N Engl J Med., 383, pp. 2603, 10.1056/NEJMoa2034577