Pooled testing of traced contacts under superspreading dynamics.

Stratis Tsirtsis, Abir De, Lars Lorch, Manuel Gomez-Rodriguez
Author Information
  1. Stratis Tsirtsis: ��ax Planck Institute for Software Systems, Kaiserslautern, Germany. ORCID
  2. Abir De: ��IT Bombay, Mumbai, India.
  3. Lars Lorch: ��TH Z��rich, Z��rich, Switzerland. ORCID
  4. Manuel Gomez-Rodriguez: ��ax Planck Institute for Software Systems, Kaiserslautern, Germany. ORCID

Abstract

Testing is recommended for all close contacts of confirmed COVID-19 patients. However, existing pooled testing methods are oblivious to the circumstances of contagion provided by contact tracing. Here, we build upon a well-known semi-adaptive pooled testing method, Dorfman's method with imperfect tests, and derive a simple pooled testing method based on dynamic programming that is specifically designed to use information provided by contact tracing. Experiments using a variety of reproduction numbers and dispersion levels, including those estimated in the context of the COVID-19 pandemic, show that the pools found using our method result in a significantly lower number of tests than those found using Dorfman's method. Our method provides the greatest competitive advantage when the number of contacts of an infected individual is small, or the distribution of secondary infections is highly overdispersed. Moreover, it maintains this competitive advantage under imperfect contact tracing and significant levels of dilution.

References

  1. Wellcome Open Res. 2020 Apr 9;5:67 [PMID: 32685698]
  2. N Engl J Med. 2020 Aug 6;383(6):e38 [PMID: 32502334]
  3. Clin Microbiol Infect. 2020 Sep;26(9):1248-1253 [PMID: 32585353]
  4. Nature. 2005 Nov 17;438(7066):355-9 [PMID: 16292310]
  5. J Med Virol. 2021 Mar;93(3):1568-1572 [PMID: 32936471]
  6. Biometrics. 2012 Mar;68(1):287-96 [PMID: 21762119]
  7. J Korean Med Sci. 2015 Nov;30(11):1701-5 [PMID: 26539018]
  8. Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22430-22435 [PMID: 32820074]
  9. Am J Infect Control. 2021 Jan;49(1):21-29 [PMID: 32659413]
  10. PLoS Comput Biol. 2021 Jul 12;17(7):e1009146 [PMID: 34252083]
  11. PLoS One. 2020 Dec 10;15(12):e0242958 [PMID: 33301459]
  12. J Clin Virol. 2020 Jul;128:104382 [PMID: 32388468]
  13. Nat Commun. 2021 Jan 15;12(1):378 [PMID: 33452267]
  14. Disaster Med Public Health Prep. 2020 Jun;14(3):e42-e43 [PMID: 32660684]
  15. PLoS Comput Biol. 2021 Jul 26;17(7):e1009149 [PMID: 34310589]
  16. J R Stat Soc Ser C Appl Stat. 2012 Mar 1;61(2):277-290 [PMID: 25035521]
  17. Stat Med. 2012 Nov 30;31(27):3261-8 [PMID: 22415972]
  18. Euro Surveill. 2015 Jun 25;20(25):14-8 [PMID: 26132768]
  19. Nat Commun. 2021 Mar 9;12(1):1524 [PMID: 33750778]
  20. Emerg Infect Dis. 2020 Jun;26(6):1059-1066 [PMID: 32187007]
  21. Int J Infect Dis. 2011 Aug;15(8):e510-3 [PMID: 21737332]
  22. J R Soc Med. 2020 Jul;113(7):245-250 [PMID: 32663428]
  23. Wellcome Open Res. 2020 Aug 6;5:186 [PMID: 33134555]
  24. BMJ Open. 2021 Jun 29;11(7):e047832 [PMID: 34187854]
  25. Sci Rep. 2020 Dec 28;10(1):22386 [PMID: 33372191]
  26. Cochrane Database Syst Rev. 2021 Mar 24;3:CD013705 [PMID: 33760236]
  27. Biometrics. 2012 Sep;68(3):793-804 [PMID: 22212007]
  28. Science. 2021 Jan 15;371(6526): [PMID: 33234698]
  29. Nature. 2021 Jan;589(7841):276-280 [PMID: 33086375]
  30. Biometrics. 2012 Jun;68(2):532-40 [PMID: 21950447]
  31. Nat Med. 2020 Nov;26(11):1714-1719 [PMID: 32943787]
  32. BMJ. 2020 May 12;369:m1808 [PMID: 32398230]
  33. IEEE Trans Netw Sci Eng. 2021 May 20;8(3):2170-2182 [PMID: 35783009]
  34. Ann Glob Health. 2020 Nov 18;86(1):148 [PMID: 33262937]
  35. PLoS Comput Biol. 2021 Mar 9;17(3):e1008688 [PMID: 33690626]
  36. Stat Med. 2021 Jul 30;40(17):3865-3880 [PMID: 33913183]
  37. Bull World Health Organ. 2020 Sep 01;98(9):590-598 [PMID: 33012859]
  38. BMC Med. 2020 Jun 3;18(1):166 [PMID: 32493466]
  39. Stat Med. 1999 May 15;18(9):1049-68 [PMID: 10378255]
  40. PLoS One. 2020 Nov 4;15(11):e0240652 [PMID: 33147228]
  41. Int J Environ Res Public Health. 2020 May 24;17(10): [PMID: 32456346]
  42. Clin Infect Dis. 2020 Nov 19;71(16):2073-2078 [PMID: 32358960]
  43. Epidemiology. 2020 Nov;31(6):832-835 [PMID: 32833708]
  44. Biometrics. 2016 Mar;72(1):299-302 [PMID: 26393800]
  45. Stat Med. 2019 Oct 30;38(24):4912-4923 [PMID: 31469188]

MeSH Term

COVID-19
Contact Tracing
Humans
Pandemics

Word Cloud

Created with Highcharts 10.0.0methodtestingcontactspooledcontacttracingusingCOVID-19providedDorfman'simperfecttestslevelsfoundnumbercompetitiveadvantageTestingrecommendedcloseconfirmedpatientsHoweverexistingmethodsobliviouscircumstancescontagionbuilduponwell-knownsemi-adaptivederivesimplebaseddynamicprogrammingspecificallydesigneduseinformationExperimentsvarietyreproductionnumbersdispersionincludingestimatedcontextpandemicshowpoolsresultsignificantlylowerprovidesgreatestinfectedindividualsmalldistributionsecondaryinfectionshighlyoverdispersedMoreovermaintainssignificantdilutionPooledtracedsuperspreadingdynamics

Similar Articles

Cited By

No available data.