Publications

Authors:

Marcolungo, Luca; Beltrami, Cristina; Degli Esposti, Chiara; Lopatriello, Giulia; Piubelli, Chiara; Mori, Antonio; Pomari, Elena; Deiana, Michela; Scarso, Salvatore; Bisoffi, Zeno; Grosso, Valentina; Cosentino, Emanuela; Maestri, Simone; Lavezzari, Denise; Iadarola, Barbara; Paterno, Marta; Segala, Elena; Giovannone, Barbara; Gallinaro, Martina; Rossato, Marzia; Delledonne, Massimo

Title:

ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections

Year:

2021

Type of item:

Articolo in Rivista

Tipologia ANVUR:

Articolo su rivista

Language:

Inglese

Referee:

No

Name of journal:

Genomics

ISSN of journal:

0888-7543

N° Volume:

113

Number or Folder:

4

Page numbers:

1628-1638

Keyword:

Genetic variants; Low-viral titer; Re-infection; SARS-CoV-2 genome sequencing; Suboptimal samples

Short description of contents:

Sequencing the SARS-CoV-2 genome from clinical samples can be challenging, especially in specimens with low viral titer. Here we report Accurate SARS-CoV-2 genome Reconstruction (ACoRE), an amplicon-based viral genome sequencing workflow for the complete and accurate reconstruction of SARS-CoV-2 sequences from clinical samples, including suboptimal ones that would usually be excluded even if unique and irreplaceable. The protocol was optimized to improve flexibility and the combination of technical replicates was established as the central strategy to achieve accurate analysis of low-titer/suboptimal samples. We demonstrated the utility of the approach by achieving complete genome reconstruction and the identification of false-positive variants in >170 clinical samples, thus avoiding the generation of inaccurate and/or incomplete sequences. Most importantly, ACoRE was crucial to identify the correct viral strain responsible of a relapse case, that would be otherwise mis-classified as a re-infection due to missing or incorrect variant identification by a standard workflow.

Product ID:

121848

Handle IRIS:

11562/1046121

Last Modified:

November 15, 2022

Bibliographic citation:

Marcolungo, Luca; Beltrami, Cristina; Degli Esposti, Chiara; Lopatriello, Giulia; Piubelli, Chiara; Mori, Antonio; Pomari, Elena; Deiana, Michela; Scarso, Salvatore; Bisoffi, Zeno; Grosso, Valentina; Cosentino, Emanuela; Maestri, Simone; Lavezzari, Denise; Iadarola, Barbara; Paterno, Marta; Segala, Elena; Giovannone, Barbara; Gallinaro, Martina; Rossato, Marzia; Delledonne, Massimo, ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections «Genomics» , vol. 113 , n. 4 , 2021 , pp. 1628-1638

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