Literature DB >> 33469026

Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy.

Claudia Alteri1, Valeria Cento1, Antonio Piralla2, Valentino Costabile3, Monica Tallarita2, Luna Colagrossi4, Silvia Renica1, Federica Giardina2, Federica Novazzi2, Stefano Gaiarsa2, Elisa Matarazzo5, Maria Antonello1, Chiara Vismara6, Roberto Fumagalli7, Oscar Massimiliano Epis8, Massimo Puoti9, Carlo Federico Perno10, Fausto Baldanti2,11.   

Abstract

From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy.

Entities:  

Year:  2021        PMID： 33469026      PMCID： PMC7815831          DOI： 10.1038/s41467-020-20688-x

Source DB:  PubMed          Journal:  Nat Commun        ISSN： 2041-1723            Impact factor:   14.919


  38 in total

1.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2011-09-08       Impact factor: 6.937

2.  Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths.

Authors:  Ernst Joachim Houtgast; Vlad-Mihai Sima; Koen Bertels; Zaid Al-Ars
Journal:  Comput Biol Chem       Date:  2018-04-12       Impact factor: 2.877

3.  The SR-rich motif in SARS-CoV nucleocapsid protein is important for virus replication.

Authors:  Shaun Tylor; Anton Andonov; Todd Cutts; Jingxin Cao; Elsey Grudesky; Gary Van Domselaar; Xuguang Li; Runtao He
Journal:  Can J Microbiol       Date:  2009-03       Impact factor: 2.419

4.  Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

Authors:  Marc A Suchard; Philippe Lemey; Guy Baele; Daniel L Ayres; Alexei J Drummond; Andrew Rambaut
Journal:  Virus Evol       Date:  2018-06-08

5.  Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide.

Authors:  Sandra Isabel; Lucía Graña-Miraglia; Jahir M Gutierrez; Cedoljub Bundalovic-Torma; Helen E Groves; Marc R Isabel; AliReza Eshaghi; Samir N Patel; Jonathan B Gubbay; Tomi Poutanen; David S Guttman; Susan M Poutanen
Journal:  Sci Rep       Date:  2020-08-20       Impact factor: 4.379

6.  Nasopharyngeal SARS-CoV-2 Load at Hospital Admission as a Predictor of Mortality.

Authors:  Claudia Alteri; Valeria Cento; Marta Vecchi; Luna Colagrossi; Diana Fanti; Chiara Vismara; Massimo Puoti; Carlo Federico Perno
Journal:  Clin Infect Dis       Date:  2021-05-18       Impact factor: 9.079

7.  Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic.

Authors:  Alessia Lai; Annalisa Bergna; Sara Caucci; Nicola Clementi; Ilaria Vicenti; Filippo Dragoni; Anna Maria Cattelan; Stefano Menzo; Angelo Pan; Annapaola Callegaro; Adriano Tagliabracci; Arnaldo Caruso; Francesca Caccuri; Silvia Ronchiadin; Claudia Balotta; Maurizio Zazzi; Emanuela Vaccher; Massimo Clementi; Massimo Galli; Gianguglielmo Zehender
Journal:  Viruses       Date:  2020-07-24       Impact factor: 5.048

8.  fastp: an ultra-fast all-in-one FASTQ preprocessor.

Authors:  Shifu Chen; Yanqing Zhou; Yaru Chen; Jia Gu
Journal:  Bioinformatics       Date:  2018-09-01       Impact factor: 6.937

9.  Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment.

Authors:  Takahiko Koyama; Dilhan Weeraratne; Jane L Snowdon; Laxmi Parida
Journal:  Pathogens       Date:  2020-04-26

10.  Evolution and epidemic spread of SARS-CoV-2 in Brazil.

Authors:  Darlan S Candido; Ingra M Claro; Jaqueline G de Jesus; William M Souza; Filipe R R Moreira; Simon Dellicour; Thomas A Mellan; Louis du Plessis; Rafael H M Pereira; Flavia C S Sales; Erika R Manuli; Julien Thézé; Luiz Almeida; Mariane T Menezes; Carolina M Voloch; Marcilio J Fumagalli; Thaís M Coletti; Camila A M da Silva; Mariana S Ramundo; Mariene R Amorim; Henrique H Hoeltgebaum; Swapnil Mishra; Mandev S Gill; Luiz M Carvalho; Lewis F Buss; Carlos A Prete; Jordan Ashworth; Helder I Nakaya; Pedro S Peixoto; Oliver J Brady; Samuel M Nicholls; Amilcar Tanuri; Átila D Rossi; Carlos K V Braga; Alexandra L Gerber; Ana Paula de C Guimarães; Nelson Gaburo; Cecila Salete Alencar; Alessandro C S Ferreira; Cristiano X Lima; José Eduardo Levi; Celso Granato; Giulia M Ferreira; Ronaldo S Francisco; Fabiana Granja; Marcia T Garcia; Maria Luiza Moretti; Mauricio W Perroud; Terezinha M P P Castiñeiras; Carolina S Lazari; Sarah C Hill; Andreza Aruska de Souza Santos; Camila L Simeoni; Julia Forato; Andrei C Sposito; Angelica Z Schreiber; Magnun N N Santos; Camila Zolini de Sá; Renan P Souza; Luciana C Resende-Moreira; Mauro M Teixeira; Josy Hubner; Patricia A F Leme; Rennan G Moreira; Maurício L Nogueira; Neil M Ferguson; Silvia F Costa; José Luiz Proenca-Modena; Ana Tereza R Vasconcelos; Samir Bhatt; Philippe Lemey; Chieh-Hsi Wu; Andrew Rambaut; Nick J Loman; Renato S Aguiar; Oliver G Pybus; Ester C Sabino; Nuno Rodrigues Faria
Journal:  Science       Date:  2020-07-23       Impact factor: 47.728
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  42 in total

1.  Epidemiological characterization of SARS-CoV-2 variants in children over the four COVID-19 waves and correlation with clinical presentation.

Authors:  Rossana Scutari; Valentino Costabile; Claudia Alteri; Luna Colagrossi; Katia Yu La Rosa; Emanuele Agolini; Valentina Lanari; Sara Chiurchiù; Lorenza Romani; Anna Hermine Markowich; Paola Bernaschi; Cristina Russo; Antonio Novelli; Stefania Bernardi; Andrea Campana; Alberto Villani; Carlo Federico Perno
Journal:  Sci Rep       Date:  2022-06-17       Impact factor: 4.996

2.  Genomic surveillance of SARS-CoV-2 in patients presenting neurological manifestations.

Authors:  Anna Vicco; Francesca Caccuri; Serena Messali; Adriana Vitiello; Aron Emmi; Claudia Del Vecchio; Alberto Reale; Arnaldo Caruso; Giancarlo Ottaviano; Carla Mucignat; Cristina Parolin; Angelo Antonini; Arianna Calistri
Journal:  PLoS One       Date:  2022-06-30       Impact factor: 3.752

3.  Epidemiologic and Genomic Analysis of the Severe Acute Respiratory Syndrome Coronavirus 2 Epidemic in the Nebraska Region of the United States, March 2020-2021.

Authors:  Jacob A Siedlik; Cynthia J Watson; Morgan A Raine; Anne V Cheng; Richard V Goering; Holly A F Stessman; Michael Belshan
Journal:  Front Microbiol       Date:  2022-05-18       Impact factor: 6.064

4.  SARS-CoV-2 transmission dynamics in Belarus in 2020 revealed by genomic and incidence data analysis.

Authors:  Alexander Kirpich; Pavel Skums; Alina Nemira; Ayotomiwa Ezekiel Adeniyi; Elena L Gasich; Kirill Y Bulda; Leonid N Valentovich; Anatoly G Krasko; Olga Glebova
Journal:  Commun Med (Lond)       Date:  2021-09-16

Review 5.  Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic.

Authors:  Stephen W Attwood; Sarah C Hill; David M Aanensen; Thomas R Connor; Oliver G Pybus
Journal:  Nat Rev Genet       Date:  2022-04-22       Impact factor: 59.581

6.  SARS-CoV-2 transmission dynamics in Belarus revealed by genomic and incidence data analysis.

Authors:  Alexander Kirpich; Pavel Skums; Alina Nemira; Ayotomiwa Ezekiel Adeniyi; Elena L Gasich; Kirill Y Bulda; Leonid N Valentovich; Anatoly G Krasko; Olga Glebova
Journal:  medRxiv       Date:  2021-04-19

7.  Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

Authors:  Bernardo Gutierrez; Sully Márquez; Belén Prado-Vivar; Mónica Becerra-Wong; Juan José Guadalupe; Darlan da Silva Candido; Juan Carlos Fernandez-Cadena; Gabriel Morey-Leon; Rubén Armas-Gonzalez; Derly Madeleiny Andrade-Molina; Alfredo Bruno; Domenica de Mora; Maritza Olmedo; Denisse Portugal; Manuel Gonzalez; Alberto Orlando; Jan Felix Drexler; Andres Moreira-Soto; Anna-Lena Sander; Sebastian Brünink; Arne Kühne; Leandro Patiño; Andrés Carrazco-Montalvo; Orson Mestanza; Jeannete Zurita; Gabriela Sevillano; Louis du Plessis; John T McCrone; Josefina Coloma; Gabriel Trueba; Verónica Barragán; Patricio Rojas-Silva; Michelle Grunauer; Moritz U G Kraemer; Nuno R Faria; Marina Escalera-Zamudio; Oliver G Pybus; Paúl Cárdenas
Journal:  medRxiv       Date:  2021-04-05

8.  Contrasting SARS-CoV-2 RNA copies and clinical symptoms in a large cohort of Colombian patients during the first wave of the COVID-19 pandemic.

Authors:  Santiago A Quiroga; Carolina Hernández; Sergio Castañeda; Paula Jimenez; Laura Vega; Marcela Gomez; David Martinez; Nathalia Ballesteros; Marina Muñoz; Claudia Cifuentes; Nathalia Sierra; Carolina Flórez; Alberto Paniz-Mondolfi; Juan David Ramírez
Journal:  Ann Clin Microbiol Antimicrob       Date:  2021-05-24       Impact factor: 3.944

9.  Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

Authors:  Bernardo Gutierrez; Sully Márquez; Belén Prado-Vivar; Mónica Becerra-Wong; Juan José Guadalupe; Darlan Da Silva Candido; Juan Carlos Fernandez-Cadena; Gabriel Morey-Leon; Rubén Armas-Gonzalez; Derly Madeleiny Andrade-Molina; Alfredo Bruno; Domenica De Mora; Maritza Olmedo; Denisse Portugal; Manuel Gonzalez; Alberto Orlando; Jan Felix Drexler; Andres Moreira-Soto; Anna-Lena Sander; Sebastian Brünink; Arne Kühne; Leandro Patiño; Andrés Carrazco-Montalvo; Orson Mestanza; Jeannete Zurita; Gabriela Sevillano; Louis Du Plessis; John T McCrone; Josefina Coloma; Gabriel Trueba; Verónica Barragán; Patricio Rojas-Silva; Michelle Grunauer; Moritz U G Kraemer; Nuno R Faria; Marina Escalera-Zamudio; Oliver G Pybus; Paúl Cárdenas
Journal:  Virus Evol       Date:  2021-06-04

10.  Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster.

Authors:  Nicole Pedro; Veronica Fernandes; Bruno Cavadas; João Tiago Guimarães; Henrique Barros; Margarida Tavares; Luisa Pereira
Journal:  Viruses       Date:  2021-06-10       Impact factor: 5.048
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