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1. Genome-based comparison between the recombinant SARS-CoV-2 XBB and its parental lineages

Author

Scarpa, Fabio, Sanna, Daria, Azzena, Ilenia, Casu, Marco, Cossu, Piero, Fiori, Pier Luigi, Benvenuto, Domenico, Imperia, Elena, Giovanetti, Marta, Ceccarelli, Giancarlo, Cauda, Roberto, Cassone, Antonio, Pascarella, Stefano, Ciccozzi, Massimo, Cauda, Roberto (ORCID:0000-0002-1498-4229), Scarpa, Fabio, Sanna, Daria, Azzena, Ilenia, Casu, Marco, Cossu, Piero, Fiori, Pier Luigi, Benvenuto, Domenico, Imperia, Elena, Giovanetti, Marta, Ceccarelli, Giancarlo, Cauda, Roberto, Cassone, Antonio, Pascarella, Stefano, Ciccozzi, Massimo, and Cauda, Roberto (ORCID:0000-0002-1498-4229)

Abstract

Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM.1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental lineages that never became dominant. Genetic analyses indicated that the recombinant XBB and its first descendant XBB.1 show an evolutionary condition typical of an evolutionary blind background with no further epidemiologically relevant descendant. Genetic variability and expansion capabilities are slightly higher than parental lineages. Bayesian Skyline Plot indicates that XBB reached its plateau around October 6, 2022 and after an initial rapid growth the viral population size did not further expand, and around November 10, 2022 its levels of genetic variability decreased. Simultaneously with the reduction of the XBB population size, an increase of the genetic variability of its first sub-lineage XBB.1 occurred, that in turn reached the plateau around November 9, 2022 showing a kind of vicariance with its direct progenitors. Structure analysis indicates that the affinity for ACE2 surface in XBB/XBB.1 RBDs is weaker than for BA.2 RBD. In conclusion, at present XBB and XBB.1 do not show evidence about a particular danger or high expansion capability. Genome-based monitoring must continue uninterrupted in order to individuate if further mutations can make XBB more dangerous or generate new subvariants with different expansion capability. This article is protected by copyright. All rights reserved.

Published
2023

2. Genome-based comparison between the recombinant SARS-CoV-2 XBB and its parental lineages

Author

Scarpa, Fabio, Sanna, Daria, Azzena, Ilenia, Casu, Marco, Cossu, Piero, Fiori, Pier Luigi, Benvenuto, Domenico, Imperia, Elena, Giovanetti, Marta, Ceccarelli, Giancarlo, Cauda, Roberto, Cassone, Antonio, Pascarella, Stefano, Ciccozzi, Massimo, Cauda, Roberto (ORCID:0000-0002-1498-4229), Scarpa, Fabio, Sanna, Daria, Azzena, Ilenia, Casu, Marco, Cossu, Piero, Fiori, Pier Luigi, Benvenuto, Domenico, Imperia, Elena, Giovanetti, Marta, Ceccarelli, Giancarlo, Cauda, Roberto, Cassone, Antonio, Pascarella, Stefano, Ciccozzi, Massimo, and Cauda, Roberto (ORCID:0000-0002-1498-4229)

Abstract

Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM.1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental lineages that never became dominant. Genetic analyses indicated that the recombinant XBB and its first descendant XBB.1 show an evolutionary condition typical of an evolutionary blind background with no further epidemiologically relevant descendant. Genetic variability and expansion capabilities are slightly higher than parental lineages. Bayesian Skyline Plot indicates that XBB reached its plateau around October 6, 2022 and after an initial rapid growth the viral population size did not further expand, and around November 10, 2022 its levels of genetic variability decreased. Simultaneously with the reduction of the XBB population size, an increase of the genetic variability of its first sub-lineage XBB.1 occurred, that in turn reached the plateau around November 9, 2022 showing a kind of vicariance with its direct progenitors. Structure analysis indicates that the affinity for ACE2 surface in XBB/XBB.1 RBDs is weaker than for BA.2 RBD. In conclusion, at present XBB and XBB.1 do not show evidence about a particular danger or high expansion capability. Genome-based monitoring must continue uninterrupted in order to individuate if further mutations can make XBB more dangerous or generate new subvariants with different expansion capability. This article is protected by copyright. All rights reserved.

Published
2023

3. Genetic and structural genome-based survey reveals the low potential for epidemiological expansion of the SARS-CoV-2 XBB.1.5 sublineage

Author

Scarpa, Fabio, Imperia, Elena, Azzena, Ilenia, Giovanetti, Marta, Benvenuto, Domenico, Locci, Chiara, Casu, Marco, Fiori, Pier Luigi, Maruotti, Antonello, Ceccarelli, Giancarlo, Borsetti, Alessandra, Caruso, Arnaldo, Cauda, Roberto, Cassone, Antonio, Via, Allegra, Pascarella, Stefano, Sanna, Daria, Ciccozzi, Massimo, Cauda, Roberto (ORCID:0000-0002-1498-4229), Scarpa, Fabio, Imperia, Elena, Azzena, Ilenia, Giovanetti, Marta, Benvenuto, Domenico, Locci, Chiara, Casu, Marco, Fiori, Pier Luigi, Maruotti, Antonello, Ceccarelli, Giancarlo, Borsetti, Alessandra, Caruso, Arnaldo, Cauda, Roberto, Cassone, Antonio, Via, Allegra, Pascarella, Stefano, Sanna, Daria, Ciccozzi, Massimo, and Cauda, Roberto (ORCID:0000-0002-1498-4229)

Abstract

not available

Published
2023

4. Genetic and Structural Data on the SARS-CoV-2 Omicron BQ.1 Variant Reveal Its Low Potential for Epidemiological Expansion

Author

Scarpa, Fabio, Sanna, Daria, Benvenuto, Domenico, Borsetti, Alessandra, Azzena, Ilenia, Casu, Marco, Fiori, Pier Luigi, Giovanetti, Marta, Maruotti, Antonello, Ceccarelli, Giancarlo, Caruso, Arnaldo, Caccuri, Francesca, Cauda, Roberto, Cassone, Antonio, Pascarella, Stefano, Ciccozzi, Massimo, Cauda, Roberto (ORCID:0000-0002-1498-4229), Scarpa, Fabio, Sanna, Daria, Benvenuto, Domenico, Borsetti, Alessandra, Azzena, Ilenia, Casu, Marco, Fiori, Pier Luigi, Giovanetti, Marta, Maruotti, Antonello, Ceccarelli, Giancarlo, Caruso, Arnaldo, Caccuri, Francesca, Cauda, Roberto, Cassone, Antonio, Pascarella, Stefano, Ciccozzi, Massimo, and Cauda, Roberto (ORCID:0000-0002-1498-4229)

Abstract

The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 has some additional spike mutations in some key antigenic sites, which confer further immune escape ability over other circulating lineages. In such a context, here, we perform a genome-based survey aimed at obtaining a complete-as-possible nuance of this rapidly evolving Omicron subvariant. Genetic data suggest that BQ.1 represents an evolutionary blind background, lacking the rapid diversification that is typical of a dangerous lineage. Indeed, the evolutionary rate of BQ.1 is very similar to that of BA.5 (7.6 x 10(-4) and 7 x 10(-4) subs/site/year, respectively), which has been circulating for several months. The Bayesian Skyline Plot reconstruction indicates a low level of genetic variability, suggesting that the peak was reached around 3 September 2022. Concerning the affinity for ACE2, structure analyses (also performed by comparing the properties of BQ.1 and BA.5 RBD) indicate that the impact of the BQ.1 mutations may be modest. Likewise, immunoinformatic analyses showed moderate differences between the BQ.1 and BA5 potential B-cell epitopes. In conclusion, genetic and structural analyses on SARS-CoV-2 BQ.1 suggest no evidence of a particularly dangerous or high expansion capability. Genome-based monitoring must continue uninterrupted for a better understanding of its descendants and all other lineages.

Published
2022

5. The value of electrostatic potentials of the spike receptor binding and N-terminal domains in addressing transmissibility and infectivity of SARS-CoV-2 variants of concern

Author

Pascarella, Stefano, Ciccozzi, Massimo, Bianchi, Martina, Benvenuto, Domenico, Cauda, Roberto, Cassone, Antonio, Cauda, Roberto (ORCID:0000-0002-1498-4229), Pascarella, Stefano, Ciccozzi, Massimo, Bianchi, Martina, Benvenuto, Domenico, Cauda, Roberto, Cassone, Antonio, and Cauda, Roberto (ORCID:0000-0002-1498-4229)

Abstract

Comparison of the surface electrostatic potential of the N-terminal (NTD) and the Receptor Binding Domains (RBD) of the Wuhan and Omicron Spikes. The entire Spikes are represented with transparent ribbon models. Only the NTD and RBD surfaces of the chain A are represented. Domain net charges are reported within parenthesis beside the domain labels. Surface color ranges from -5.0 (red) to + 5.0 (blue) kT/e. Image, graphical abstract

Published
2022

6. COVID-19 atypical Parsonage-Turner syndrome: a case report

Author

Zazzara, Maria Beatrice, Modoni, Anna, Bizzarro, Alessandra, Lauria, Alessandra, Ciciarello, Francesca, Pais, Cristina, Galluzzo, Vincenzo, Landi, Francesco, Tostato, Matteo, Gremese, Elisa, Bernabei, Roberto, Fantoni, Massimo, Gasbarrini, Antonio, Settanni, Carlo Romano, Porcari, Serena, Benvenuto, Francesca, Bramato, Giulia, Brandi, Vincenzo, Carfì, Angelo, Lo Monaco, Maria Rita, Martone, Anna Maria, Marzetti, Emanuele, Napolitano, Carmen, Pagano, Francesco Cosimo, Rocchi, Sara, Rota, Elisabetta, Salerno, Andrea Maria, Tosato, Matteo, Tritto, Marcello, Calvani, Riccardo, Catalano, Lucio, Picca, Anna, Savera, Giulia, Cauda, Roberto, Murri, Rita, Cingolani, Antonella, Ventura, Giulio, Taddei, Eleonora, Moschese, Davide, Ciccullo, Arturo, Stella, Leonardo, Addolorato, Giovanni, Franceschi, Francesco, Mingrone, Gertrude, Zocco, Maria Assunta, Sanguinetti, Maurizio, Cattani Franchi, Paola, Marchetti, Simona, Posteraro, Brunella, Sali, Michela, Rizzo, Stanislao, Savastano, Maria Cristina, Gambini, Gloria, Cozzupoli, Maria Grazia, Culiersi, Carola, Passali, Giulio Cesare, Paludetti, Gaetano, Galli, Jacopo, Crudo, Fabrizio, Di Cintio, Giovanni, Longobardi, Ylenia, Tricarico, Laura, Santantonio, Mariaconsiglia, Di Cesare, Tiziana, Guarino, Mariateresa, Corbò, Marco, Settimi, Stefano, Mele, Dario Antonio, Brigato, Francesca, Buonsenso, Danilo, Valentini, Piero, Sinatti, Dario, De Rose, Gabriella, Richeldi, Luca, Lombardi, Francesco, Calabrese, Angelo, Varone, Francesco, Leone, Paolo Maria, Siciliano, Matteo, Corbo, Giuseppe Maria, Montemurro, Giuliano, Calvello, Mariarosaria, Intini, Enrica, Simonetti, Jacopo, Pasciuto, Giuliana, Adiletta, Veronica, Sofia, Carmelo, Licata, Maria Angela Vittoria Anna Chiara, Sani, Gabriele, Janiri, Delfina, Simonetti, Alessio, Modica, Marco, Montanari, Silvia, Catinari, Antonello, Terenzi, Beatrice, Natale, Luigi, Larici, Anna Rita, Marano, Riccardo, Pirronti, Tommaso, Infante, Amato, Paglionico, Annamaria, Petricca, Luca, Tolusso, Barbara, Alivernini, Stefano, Di Mario, Clara, Santoliquido, Angelo, Santoro, Luca, Nesci, Antonio, Di Giorgio, Angela, Null, Null, Landi, Francesco (ORCID:0000-0002-3472-1389), Gremese, Elisa (ORCID:0000-0002-2248-1058), Bernabei, Roberto (ORCID:0000-0002-9197-004X), Fantoni, Massimo (ORCID:0000-0001-6913-8460), Gasbarrini, Antonio (ORCID:0000-0002-7278-4823), Lo Monaco, Maria Rita (ORCID:0000-0002-1457-7981), Marzetti, Emanuele (ORCID:0000-0001-9567-6983), Pagano, Francesco, Salerno, Andrea, Calvani, Riccardo (ORCID:0000-0001-5472-2365), Cauda, Roberto (ORCID:0000-0002-1498-4229), Murri, Rita (ORCID:0000-0003-4263-7854), Cingolani, Antonella (ORCID:0000-0002-3793-2755), Ventura, Giulio (ORCID:0000-0002-0304-7264), Addolorato, Giovanni (ORCID:0000-0002-1522-9946), Zocco, Maria Assunta (ORCID:0000-0002-0814-9542), Sanguinetti, Maurizio (ORCID:0000-0002-9780-7059), Cattani, Paola (ORCID:0000-0003-4678-4763), Posteraro, Brunella (ORCID:0000-0002-1663-7546), Sali, Michela (ORCID:0000-0003-3609-2990), Rizzo, Stanislao (ORCID:0000-0001-6302-063X), Savastano, Maria Cristina (ORCID:0000-0003-1397-4333), Passali, Giulio Cesare (ORCID:0000-0002-8176-0962), Paludetti, Gaetano (ORCID:0000-0003-2480-1243), Galli, Jacopo (ORCID:0000-0001-6353-6249), Settimi, Stefano (ORCID:0000-0003-0104-1501), Mele, Dario, Valentini, Piero (ORCID:0000-0001-6095-9510), Richeldi, Luca (ORCID:0000-0001-8594-1448), Corbo, Giuseppe Maria (ORCID:0000-0002-8104-4659), Licata, Maria Angela, Sani, Gabriele (ORCID:0000-0002-9767-8752), Natale, Luigi (ORCID:0000-0002-7949-5119), Larici, Anna Rita (ORCID:0000-0002-1882-6244), Marano, Riccardo (ORCID:0000-0003-2710-2093), Pirronti, Tommaso (ORCID:0000-0003-3138-4097), Tolusso, Barbara (ORCID:0000-0002-9108-6609), Alivernini, Stefano (ORCID:0000-0002-7383-4212), Santoliquido, Angelo (ORCID:0000-0003-1539-4017), Zazzara, Maria Beatrice, Modoni, Anna, Bizzarro, Alessandra, Lauria, Alessandra, Ciciarello, Francesca, Pais, Cristina, Galluzzo, Vincenzo, Landi, Francesco, Tostato, Matteo, Gremese, Elisa, Bernabei, Roberto, Fantoni, Massimo, Gasbarrini, Antonio, Settanni, Carlo Romano, Porcari, Serena, Benvenuto, Francesca, Bramato, Giulia, Brandi, Vincenzo, Carfì, Angelo, Lo Monaco, Maria Rita, Martone, Anna Maria, Marzetti, Emanuele, Napolitano, Carmen, Pagano, Francesco Cosimo, Rocchi, Sara, Rota, Elisabetta, Salerno, Andrea Maria, Tosato, Matteo, Tritto, Marcello, Calvani, Riccardo, Catalano, Lucio, Picca, Anna, Savera, Giulia, Cauda, Roberto, Murri, Rita, Cingolani, Antonella, Ventura, Giulio, Taddei, Eleonora, Moschese, Davide, Ciccullo, Arturo, Stella, Leonardo, Addolorato, Giovanni, Franceschi, Francesco, Mingrone, Gertrude, Zocco, Maria Assunta, Sanguinetti, Maurizio, Cattani Franchi, Paola, Marchetti, Simona, Posteraro, Brunella, Sali, Michela, Rizzo, Stanislao, Savastano, Maria Cristina, Gambini, Gloria, Cozzupoli, Maria Grazia, Culiersi, Carola, Passali, Giulio Cesare, Paludetti, Gaetano, Galli, Jacopo, Crudo, Fabrizio, Di Cintio, Giovanni, Longobardi, Ylenia, Tricarico, Laura, Santantonio, Mariaconsiglia, Di Cesare, Tiziana, Guarino, Mariateresa, Corbò, Marco, Settimi, Stefano, Mele, Dario Antonio, Brigato, Francesca, Buonsenso, Danilo, Valentini, Piero, Sinatti, Dario, De Rose, Gabriella, Richeldi, Luca, Lombardi, Francesco, Calabrese, Angelo, Varone, Francesco, Leone, Paolo Maria, Siciliano, Matteo, Corbo, Giuseppe Maria, Montemurro, Giuliano, Calvello, Mariarosaria, Intini, Enrica, Simonetti, Jacopo, Pasciuto, Giuliana, Adiletta, Veronica, Sofia, Carmelo, Licata, Maria Angela Vittoria Anna Chiara, Sani, Gabriele, Janiri, Delfina, Simonetti, Alessio, Modica, Marco, Montanari, Silvia, Catinari, Antonello, Terenzi, Beatrice, Natale, Luigi, Larici, Anna Rita, Marano, Riccardo, Pirronti, Tommaso, Infante, Amato, Paglionico, Annamaria, Petricca, Luca, Tolusso, Barbara, Alivernini, Stefano, Di Mario, Clara, Santoliquido, Angelo, Santoro, Luca, Nesci, Antonio, Di Giorgio, Angela, Null, Null, Landi, Francesco (ORCID:0000-0002-3472-1389), Gremese, Elisa (ORCID:0000-0002-2248-1058), Bernabei, Roberto (ORCID:0000-0002-9197-004X), Fantoni, Massimo (ORCID:0000-0001-6913-8460), Gasbarrini, Antonio (ORCID:0000-0002-7278-4823), Lo Monaco, Maria Rita (ORCID:0000-0002-1457-7981), Marzetti, Emanuele (ORCID:0000-0001-9567-6983), Pagano, Francesco, Salerno, Andrea, Calvani, Riccardo (ORCID:0000-0001-5472-2365), Cauda, Roberto (ORCID:0000-0002-1498-4229), Murri, Rita (ORCID:0000-0003-4263-7854), Cingolani, Antonella (ORCID:0000-0002-3793-2755), Ventura, Giulio (ORCID:0000-0002-0304-7264), Addolorato, Giovanni (ORCID:0000-0002-1522-9946), Zocco, Maria Assunta (ORCID:0000-0002-0814-9542), Sanguinetti, Maurizio (ORCID:0000-0002-9780-7059), Cattani, Paola (ORCID:0000-0003-4678-4763), Posteraro, Brunella (ORCID:0000-0002-1663-7546), Sali, Michela (ORCID:0000-0003-3609-2990), Rizzo, Stanislao (ORCID:0000-0001-6302-063X), Savastano, Maria Cristina (ORCID:0000-0003-1397-4333), Passali, Giulio Cesare (ORCID:0000-0002-8176-0962), Paludetti, Gaetano (ORCID:0000-0003-2480-1243), Galli, Jacopo (ORCID:0000-0001-6353-6249), Settimi, Stefano (ORCID:0000-0003-0104-1501), Mele, Dario, Valentini, Piero (ORCID:0000-0001-6095-9510), Richeldi, Luca (ORCID:0000-0001-8594-1448), Corbo, Giuseppe Maria (ORCID:0000-0002-8104-4659), Licata, Maria Angela, Sani, Gabriele (ORCID:0000-0002-9767-8752), Natale, Luigi (ORCID:0000-0002-7949-5119), Larici, Anna Rita (ORCID:0000-0002-1882-6244), Marano, Riccardo (ORCID:0000-0003-2710-2093), Pirronti, Tommaso (ORCID:0000-0003-3138-4097), Tolusso, Barbara (ORCID:0000-0002-9108-6609), Alivernini, Stefano (ORCID:0000-0002-7383-4212), and Santoliquido, Angelo (ORCID:0000-0003-1539-4017)

Abstract

Background Neurological manifestations of Sars-CoV-2 infection have been described since March 2020 and include both central and peripheral nervous system manifestations. Neurological symptoms, such as headache or persistent loss of smell and taste, have also been documented in COVID-19 long-haulers. Moreover, long lasting fatigue, mild cognitive impairment and sleep disorders appear to be frequent long term neurological manifestations after hospitalization due to COVID-19. Less is known in relation to peripheral nerve injury related to Sars-CoV-2 infection. Case presentation We report the case of a 47-year-old female presenting with a unilateral chest pain radiating to the left arm lasting for more than two months after recovery from Sars-CoV-2 infection. After referral to our post-acute outpatient service for COVID-19 long haulers, she was diagnosed with a unilateral, atypical, pure sensory brachial plexus neuritis potentially related to COVID-19, which occurred during the acute phase of a mild Sars-CoV-2 infection and persisted for months after resolution of the infection. Conclusions We presented a case of atypical Parsonage-Turner syndrome potentially triggered by Sars-CoV-2 infection, with symptoms and repercussion lasting after viral clearance. A direct involvement of the virus remains uncertain, and the physiopathology is unclear. The treatment of COVID-19 and its long-term consequences represents a relatively new challenge for clinicians and health care providers. A multidisciplinary approach to following-up COVID-19 survivors is strongly advised.

Published
2022

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