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A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual.
J Transl Med. 2020 09 23; 18(1):362.JT

Abstract

BACKGROUND

Since the first outbreak of SARS-CoV-2, the clinical characteristics of the Coronavirus Disease 2019 (COVID-19) have been progressively changed. Data reporting a viral intra-host and inter-host evolution favouring the appearance of mild SARS-CoV-2 strains are since being accumulating. To better understand the evolution of SARS-CoV-2 pathogenicity and its adaptation to the host, it is therefore crucial to investigate the genetic and phenotypic characteristics of SARS-CoV-2 strains circulating lately in the epidemic.

METHODS

Nasopharyngeal swabs have been analyzed for viral load in the early (March 2020) and late (May 2020) phases of epidemic in Brescia, Italy. Isolation of SARS-CoV-2 from 2 high viral load specimens identified on March 9 (AP66) and on May 8 (GZ69) was performed on Vero E6 cells. Amount of virus released was assessed by quantitative PCR. Genotypic characterization of AP66 and GZ69 was performed by next generation sequencing followed by an in-depth in silico analysis of nucleotide mutations.

RESULTS

The SARS-CoV-2 GZ69 strain, isolated in May from an asymptomatic healthcare worker, showed an unprecedented capability of replication in Vero E6 cells in the absence of any evident cytopathic effect. Vero E6 subculturing, up to passage 4, showed that SARS-CoV-2 GZ69 infection was as productive as the one sustained by the cytopathic strain AP66. Whole genome sequencing of the persistently replicating SARS-CoV-2 GZ69 has shown that this strain differs from the early AP66 variant in 9 nucleotide positions (C2939T; C3828T; G21784T; T21846C; T24631C; G28881A; G28882A; G28883C; G29810T) which lead to 6 non-synonymous substitutions spanning on ORF1ab (P892S; S1188L), S (K74N; I95T) and N (R203K, G204R) proteins.

CONCLUSIONS

Identification of the peculiar SARS-CoV-2 GZ69 strain in the late Italian epidemic highlights the need to better characterize viral variants circulating among asymptomatic or paucisymptomatic individuals. The current approach could unravel the ways for future studies aimed at analyzing the selection process which favours viral mutations in the human host.

Authors+Show Affiliations

Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio De Janeiro, Brazil.Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy.Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy.Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy. arnaldo.caruso@unibs.it.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32967693

Citation

Caccuri, Francesca, et al. "A Persistently Replicating SARS-CoV-2 Variant Derived From an Asymptomatic Individual." Journal of Translational Medicine, vol. 18, no. 1, 2020, p. 362.
Caccuri F, Zani A, Messali S, et al. A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. J Transl Med. 2020;18(1):362.
Caccuri, F., Zani, A., Messali, S., Giovanetti, M., Bugatti, A., Campisi, G., Filippini, F., Scaltriti, E., Ciccozzi, M., Fiorentini, S., & Caruso, A. (2020). A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. Journal of Translational Medicine, 18(1), 362. https://doi.org/10.1186/s12967-020-02535-1
Caccuri F, et al. A Persistently Replicating SARS-CoV-2 Variant Derived From an Asymptomatic Individual. J Transl Med. 2020 09 23;18(1):362. PubMed PMID: 32967693.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. AU - Caccuri,Francesca, AU - Zani,Alberto, AU - Messali,Serena, AU - Giovanetti,Marta, AU - Bugatti,Antonella, AU - Campisi,Giovanni, AU - Filippini,Federica, AU - Scaltriti,Erika, AU - Ciccozzi,Massimo, AU - Fiorentini,Simona, AU - Caruso,Arnaldo, Y1 - 2020/09/23/ PY - 2020/07/04/received PY - 2020/09/15/accepted PY - 2020/9/24/entrez PY - 2020/9/25/pubmed PY - 2020/10/3/medline KW - Asymptomatic infection KW - COVID-19 epidemic KW - Genetic variation KW - SARS-CoV-2 KW - Virus isolate KW - Virus persistence SP - 362 EP - 362 JF - Journal of translational medicine JO - J Transl Med VL - 18 IS - 1 N2 - BACKGROUND: Since the first outbreak of SARS-CoV-2, the clinical characteristics of the Coronavirus Disease 2019 (COVID-19) have been progressively changed. Data reporting a viral intra-host and inter-host evolution favouring the appearance of mild SARS-CoV-2 strains are since being accumulating. To better understand the evolution of SARS-CoV-2 pathogenicity and its adaptation to the host, it is therefore crucial to investigate the genetic and phenotypic characteristics of SARS-CoV-2 strains circulating lately in the epidemic. METHODS: Nasopharyngeal swabs have been analyzed for viral load in the early (March 2020) and late (May 2020) phases of epidemic in Brescia, Italy. Isolation of SARS-CoV-2 from 2 high viral load specimens identified on March 9 (AP66) and on May 8 (GZ69) was performed on Vero E6 cells. Amount of virus released was assessed by quantitative PCR. Genotypic characterization of AP66 and GZ69 was performed by next generation sequencing followed by an in-depth in silico analysis of nucleotide mutations. RESULTS: The SARS-CoV-2 GZ69 strain, isolated in May from an asymptomatic healthcare worker, showed an unprecedented capability of replication in Vero E6 cells in the absence of any evident cytopathic effect. Vero E6 subculturing, up to passage 4, showed that SARS-CoV-2 GZ69 infection was as productive as the one sustained by the cytopathic strain AP66. Whole genome sequencing of the persistently replicating SARS-CoV-2 GZ69 has shown that this strain differs from the early AP66 variant in 9 nucleotide positions (C2939T; C3828T; G21784T; T21846C; T24631C; G28881A; G28882A; G28883C; G29810T) which lead to 6 non-synonymous substitutions spanning on ORF1ab (P892S; S1188L), S (K74N; I95T) and N (R203K, G204R) proteins. CONCLUSIONS: Identification of the peculiar SARS-CoV-2 GZ69 strain in the late Italian epidemic highlights the need to better characterize viral variants circulating among asymptomatic or paucisymptomatic individuals. The current approach could unravel the ways for future studies aimed at analyzing the selection process which favours viral mutations in the human host. SN - 1479-5876 UR - https://www.unboundmedicine.com/medline/citation/32967693/A_persistently_replicating_SARS_CoV_2_variant_derived_from_an_asymptomatic_individual_ L2 - https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-020-02535-1 DB - PRIME DP - Unbound Medicine ER -