Early Diffusion of SARS-CoV-2 Infection in the Inner Area of the Italian Sardinia Island.
COVID-19
SARS-CoV-2
Sardinia Island
epidemiology
genome sequencing
molecular characterization
pandemic
phylogeny
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2020
2020
Historique:
received:
11
11
2020
accepted:
22
12
2020
entrez:
1
3
2021
pubmed:
2
3
2021
medline:
2
3
2021
Statut:
epublish
Résumé
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the coronavirus disease 2019 (COVID-19) pandemic, which started as a severe pneumonia outbreak in Wuhan, China, in December 2019. Italy has been the first European country affected by the pandemic, registering a total of 300,363 cases and 35,741 deaths until September 24, 2020. The geographical distribution of SARS-CoV-2 in Italy during early 2020 has not been homogeneous, including regions severely affected as well as administrative areas being only slightly interested by the infection. Among the latter, Sardinia represents one of the lowest incidence areas likely due to its insular nature. Next-generation sequencing of a small number of complete viral genomes from clinical samples and their virologic and phylogenetic characterization was performed. We provide a first overview of the SARS-CoV-2 genomic diversity in Sardinia in the early phase of the March-May 2020 pandemic based on viral genomes isolated in the most inner regional hospital of the island. Our analysis revealed a remarkable genetic diversity in local SARS-CoV-2 viral genomes, showing the presence of at least four different clusters that can be distinguished by specific amino acid substitutions. Based on epidemiological information, these sequences can be linked to at least eight different clusters of infection, four of which likely originates from imported cases. In addition, the presence of amino acid substitutions that were not previously reported in Italian patients has been observed, asking for further investigations in a wider population to assess their prevalence and dynamics of emergence during the pandemic. The present study provides a snapshot of the initial phases of the SARS-CoV-2 infection in inner area of the Sardinia Island, showing an unexpected genomic diversity.
Sections du résumé
BACKGROUND
BACKGROUND
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the coronavirus disease 2019 (COVID-19) pandemic, which started as a severe pneumonia outbreak in Wuhan, China, in December 2019. Italy has been the first European country affected by the pandemic, registering a total of 300,363 cases and 35,741 deaths until September 24, 2020. The geographical distribution of SARS-CoV-2 in Italy during early 2020 has not been homogeneous, including regions severely affected as well as administrative areas being only slightly interested by the infection. Among the latter, Sardinia represents one of the lowest incidence areas likely due to its insular nature.
METHODS
METHODS
Next-generation sequencing of a small number of complete viral genomes from clinical samples and their virologic and phylogenetic characterization was performed.
RESULTS
RESULTS
We provide a first overview of the SARS-CoV-2 genomic diversity in Sardinia in the early phase of the March-May 2020 pandemic based on viral genomes isolated in the most inner regional hospital of the island. Our analysis revealed a remarkable genetic diversity in local SARS-CoV-2 viral genomes, showing the presence of at least four different clusters that can be distinguished by specific amino acid substitutions. Based on epidemiological information, these sequences can be linked to at least eight different clusters of infection, four of which likely originates from imported cases. In addition, the presence of amino acid substitutions that were not previously reported in Italian patients has been observed, asking for further investigations in a wider population to assess their prevalence and dynamics of emergence during the pandemic.
CONCLUSION
CONCLUSIONS
The present study provides a snapshot of the initial phases of the SARS-CoV-2 infection in inner area of the Sardinia Island, showing an unexpected genomic diversity.
Identifiants
pubmed: 33643227
doi: 10.3389/fmicb.2020.628194
pmc: PMC7907441
doi:
Types de publication
Journal Article
Langues
eng
Pagination
628194Informations de copyright
Copyright © 2021 Piras, Grandi, Monne, Asproni, Fancello, Fiamma, Mameli, Casu, lo Maglio, Palmas and Tramontano.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Front Microbiol. 2020 Sep 25;11:593548
pubmed: 33101264
Int J Infect Dis. 2020 Aug;97:240-244
pubmed: 32544668
N Engl J Med. 2020 Feb 20;382(8):727-733
pubmed: 31978945
One Health. 2020 Apr 19;10:100135
pubmed: 32313828
J Neurovirol. 2020 Dec;26(6):834-837
pubmed: 32901393
Acta Pharmacol Sin. 2020 Sep;41(9):1167-1177
pubmed: 32737471
J Neurovirol. 2020 Jun;26(3):311-323
pubmed: 32548750
BMC Bioinformatics. 2007 Nov 22;8:460
pubmed: 18034891
Science. 2020 Jul 31;369(6503):582-587
pubmed: 32513865
Int J Clin Pract. 2020 Aug;74(8):e13525
pubmed: 32374903
Microbes Infect. 2020 Nov - Dec;22(10):598-607
pubmed: 33049387
Science. 2020 May 15;368(6492):779-782
pubmed: 32277040
Viruses. 2020 Mar 27;12(4):
pubmed: 32230900
Nature. 2020 Oct 26;:
pubmed: 33106671
Brief Bioinform. 2008 Jul;9(4):299-306
pubmed: 18417537
Nature. 2020 Mar;579(7798):265-269
pubmed: 32015508
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
BMC Genomics. 2016 Sep 05;17:708
pubmed: 27595578
Cell Rep. 2021 Jan 12;34(2):108630
pubmed: 33417835
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427
J Transl Med. 2020 Apr 22;18(1):179
pubmed: 32321524