Best Molecular Tools to Investigate Coronavirus Diversity in Mammals: A Comparison.
Alphacoronavirus
/ genetics
Animals
Animals, Wild
/ virology
Betacoronavirus
/ genetics
COVID-19
/ veterinary
Chiroptera
/ virology
Coronavirus Infections
/ veterinary
Deltacoronavirus
/ genetics
Gammacoronavirus
/ genetics
Genome, Viral
/ genetics
Humans
Livestock
/ virology
Rodentia
/ virology
SARS-CoV-2
/ genetics
BoCoV
CaCoV
RT-PCR
SARS-CoV-2
coronavirus
pan-CoV
surveillance
Journal
Viruses
ISSN: 1999-4915
Titre abrégé: Viruses
Pays: Switzerland
ID NLM: 101509722
Informations de publication
Date de publication:
01 10 2021
01 10 2021
Historique:
received:
27
08
2021
revised:
21
09
2021
accepted:
27
09
2021
entrez:
26
10
2021
pubmed:
27
10
2021
medline:
11
11
2021
Statut:
epublish
Résumé
Coronaviruses (CoVs) are widespread and highly diversified in wildlife and domestic mammals and can emerge as zoonotic or epizootic pathogens and consequently host shift from these reservoirs, highlighting the importance of veterinary surveillance. All genera can be found in mammals, with α and β showing the highest frequency and diversification. The aims of this study were to review the literature for features of CoV surveillance in animals, to test widely used molecular protocols, and to identify the most effective one in terms of spectrum and sensitivity. We combined a literature review with analyses in silico and in vitro using viral strains and archive field samples. We found that most protocols defined as pan-coronavirus are strongly biased towards α- and β-CoVs and show medium-low sensitivity. The best results were observed using our new protocol, showing LoD 100 PFU/mL for SARS-CoV-2, 50 TCID
Identifiants
pubmed: 34696405
pii: v13101975
doi: 10.3390/v13101975
pmc: PMC8538982
pii:
doi:
Types de publication
Comparative Study
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Ministero della Salute
ID : IZSVE 01/20 RCS and ID 95 ConVErgence
Organisme : Horizon 2020
ID : 862605 ID 95 ConVErgence.
Références
Science. 2020 Oct 9;370(6513):172-173
pubmed: 33033207
J Virol. 2011 Dec;85(23):12815-20
pubmed: 21957308
Viruses. 2021 May 18;13(5):
pubmed: 34070175
J Mol Diagn. 2010 Jan;12(1):109-17
pubmed: 19948821
Virology. 2007 Jun 20;363(1):1-10
pubmed: 17434558
J Virol. 2005 Feb;79(3):1595-604
pubmed: 15650185
Lancet Infect Dis. 2013 Oct;13(10):859-66
pubmed: 23933067
J Virol. 1998 May;72(5):4508-14
pubmed: 9557750
Viruses. 2010 Aug;2(8):1804-20
pubmed: 21994708
Vet Clin North Am Food Anim Pract. 2010 Mar;26(1):123-46, table of contents
pubmed: 20117547
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5
pubmed: 27095192
Viruses. 2021 Apr 01;13(4):
pubmed: 33915875
PLoS One. 2015 Jun 08;10(6):e0129256
pubmed: 26053682
Curr Opin Virol. 2019 Feb;34:39-49
pubmed: 30654269
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
Euro Surveill. 2020 Jan;25(3):
pubmed: 31992387
J Virol. 2012 Apr;86(7):3995-4008
pubmed: 22278237
Viruses. 2019 Dec 10;11(12):
pubmed: 31835559
Nature. 2017 Jun 29;546(7660):646-650
pubmed: 28636590
J Gen Virol. 2006 Sep;87(Pt 9):2461-2466
pubmed: 16894183
Nature. 2018 Apr;556(7700):255-258
pubmed: 29618817
Infect Genet Evol. 2018 Mar;58:279-289
pubmed: 29355607
N Engl J Med. 2012 Nov 8;367(19):1814-20
pubmed: 23075143
N Engl J Med. 2003 May 15;348(20):1967-76
pubmed: 12690091
J Clin Microbiol. 2007 Mar;45(3):1049-52
pubmed: 17229859
Genome Announc. 2014 Apr 10;2(2):
pubmed: 24723704
Virology. 2007 Oct 25;367(2):428-39
pubmed: 17617433
J Virol Methods. 2008 Aug;151(2):167-71
pubmed: 18579223
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9
pubmed: 18424797
Viruses. 2019 Oct 24;11(11):
pubmed: 31652964
Virus Evol. 2020 Nov 21;6(2):veaa078
pubmed: 33318860
Virus Evol. 2017 Jun 12;3(1):vex012
pubmed: 28630747
Science. 2016 Jan 1;351(6268):81-4
pubmed: 26678874
J Gen Virol. 2005 Jun;86(Pt 6):1597-1607
pubmed: 15914837
mBio. 2010 Oct 12;1(4):
pubmed: 21063474
Nature. 2020 Dec;588(7836):E6
pubmed: 33199918
J Mol Biol. 2006 Dec 15;364(5):964-73
pubmed: 17054987
J Virol. 2008 May;82(10):5084-8
pubmed: 18353961
J Virol. 2015 Dec;89(23):11858-70
pubmed: 26378164
Biosaf Health. 2020 Mar;2(1):6-8
pubmed: 32562482
Vet Rec. 2020 Mar 14;186(10):323
pubmed: 32165523
Nat Rev Microbiol. 2019 Mar;17(3):181-192
pubmed: 30531947
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):14040-5
pubmed: 16169905
J Virol. 2005 Jan;79(2):884-95
pubmed: 15613317
Exp Biol Med (Maywood). 2009 Oct;234(10):1117-27
pubmed: 19546349
J Virol Methods. 2018 Jun;256:116-122
pubmed: 29499225
Virol J. 2015 Dec 22;12:193
pubmed: 26689811
J Wildl Dis. 2015 Jan;51(1):218-21
pubmed: 25380364
J Virol. 2005 Feb;79(4):2001-9
pubmed: 15681402
FEMS Microbiol Rev. 2020 Sep 1;44(5):631-644
pubmed: 32672814
Transbound Emerg Dis. 2018 Jun;65(3):660-675
pubmed: 29392870
Antiviral Res. 2014 Jan;101:45-56
pubmed: 24184128
J Clin Virol. 2020 Jul;128:104391
pubmed: 32403008
Virol J. 2020 Nov 23;17(1):183
pubmed: 33225958
mSphere. 2020 Jan 29;5(1):
pubmed: 31996413
Sci China Life Sci. 2016 Jun;59(6):604-14
pubmed: 27125516
Transbound Emerg Dis. 2015 Dec;62(6):575-80
pubmed: 26250097
J Gen Virol. 2020 Dec;101(12):1261-1269
pubmed: 32902374