4.7 Article

SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels

Related references

Note: Only part of the references are listed.
Review Public, Environmental & Occupational Health

COVID-19 Models for Hospital Surge Capacity Planning: A Systematic Review

Michael G. Klein et al.

Summary: This review focused on models for projecting caseload and hospital capacity requirements over time for COVID-19 preparedness. The study identified 6 models that met criteria, providing valuable information for healthcare professionals and emergency response personnel in scenario-based planning for similar outbreaks.

DISASTER MEDICINE AND PUBLIC HEALTH PREPAREDNESS (2022)

Review Biochemical Research Methods

Bioinformatics resources for SARS-CoV-2 discovery and surveillance

Tao Hu et al.

Summary: In early 2020, the novel coronavirus responsible for the pneumonia outbreak in Wuhan was identified using NGS and bioinformatics pipelines. These technologies are now being used globally for genomic surveillance of SARS-CoV-2, tracking its spread, evolution, and global variation patterns, with a focus on technical advancements needed for future infectious disease outbreaks.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Medicine, General & Internal

6-month consequences of COVID-19 in patients discharged from hospital: a cohort study (Publication with Expression of Concern. See vol. 401, pg. 90, 2023)

Chaolin Huang et al.

Summary: This study aimed to investigate the long-term health consequences of discharged COVID-19 patients and associated risk factors, particularly disease severity. Patients with more severe illness during hospitalization showed more severe impaired pulmonary diffusion capacities and abnormal chest imaging manifestations, highlighting the need for targeted interventions for long-term recovery.

LANCET (2021)

News Item Multidisciplinary Sciences

COVID-19 New mutations raise specter of 'immune escape'

Kai Kupferschmidt

SCIENCE (2021)

Article Multidisciplinary Sciences

New coronavirus variants could cause more reinfections, require updated vaccines

Kai Kupferschmidt

SCIENCE (2021)

Article Environmental Sciences

SARS-CoV-2 has been circulating in northern Italy since December 2019: Evidence from environmental monitoring

Giuseppina La Rosa et al.

Summary: Italy had SARS-CoV-2 circulating as early as the end of 2019, with the virus spreading in different geographic regions simultaneously. The study emphasizes the importance of environmental surveillance as an early warning system to monitor virus levels and identify outbreaks before they are officially reported to the healthcare system.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

Article Multidisciplinary Sciences

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

Claudia Alteri et al.

Summary: The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Using whole genome sequencing, researchers found multiple virus introductions into the region with transmission occurring before the first case was detected.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

Constantinos Kurt Wibmer et al.

Summary: The SARS-CoV-2 virus in the B.1.351 variant discovered in South Africa can evade neutralization by most antibodies when expressed, but does not affect binding by convalescent plasma. This suggests the potential for reinfection with antigenically distinct variants and predicts reduced efficacy of spike-based vaccines.

NATURE MEDICINE (2021)

Article Biochemistry & Molecular Biology

Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera

Xuping Xie et al.

Summary: The study found that human sera from recipients of the BNT162b2 vaccine can neutralize SARS-CoV-2 viruses containing key spike mutations from the newly emerged UK and SA variants.

NATURE MEDICINE (2021)

Article Multidisciplinary Sciences

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Nicholas G. Davies et al.

Summary: A new variant of SARS-CoV-2 has emerged in England, with a higher reproduction number and potential for large resurgences of COVID-19 cases. Without stringent control measures, it is projected that COVID-19 hospitalizations and deaths in England for the first 6 months of 2021 will exceed those in 2020. The variant has spread globally and exhibited similar transmission increases in Denmark, Switzerland, and the United States.

SCIENCE (2021)

Article Medicine, General & Internal

Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study

Robert Challen et al.

Summary: The study found that the mortality hazard ratio associated with infection with VOC-202012/1 compared with previously circulating variants was 1.64, indicating an increase in deaths from 2.5 to 4.1 per 1000 detected cases in comparatively low risk group of covid-19 patients in the community. This suggests that infection with VOC-202012/1 may lead to substantial additional mortality compared with previously circulating variants, impacting healthcare capacity planning and control policies.

BMJ-BRITISH MEDICAL JOURNAL (2021)

Article Immunology

Variant analysis of SARS-CoV-2 genomes in the Middle East

Khalid Mubarak Bindayna et al.

Summary: The analysis of genomic variants in the Middle East region revealed that Iran was likely the main source of introducing COVID-19 to other countries in the Middle East. Some countries showed evidence of novel mutations and unique strains. The study indicates that increased time in small populations can contribute to more unique genomes.

MICROBIAL PATHOGENESIS (2021)

Article Virology

Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy

Francesca Di Giallonardo et al.

Summary: Italy's second wave of SARS-CoV-2 has caused significant impacts, with different virus lineages emerging independently multiple times despite lockdown measures. The dominant variant shifted from B.1.177 to the 'variant of concern' B.1.1.7 since January 2021. The sudden increase of lineage P.1 from December 2020 onwards was likely caused by a single introduction into Italy, emphasizing the importance of international importations in driving new lineages.

VIRUSES-BASEL (2021)

Editorial Material Critical Care Medicine

SARS-CoV-2 evolution and vaccines: cause for concern?

Thomas C. Williams et al.

LANCET RESPIRATORY MEDICINE (2021)

Article Biochemical Research Methods

Data-driven identification of SARS-CoV-2 subpopulations using PhenoGraph and binary-coded genomic data

Zhi-Kai Yang et al.

Summary: The study analyzed the genomic sequences of hundreds of thousands of SARS-CoV-2 isolates, successfully identifying 303 subpopulations and revealing a gradual decrease in GC content in the viral genome, indicating stability in mutations. The research results not only provide a more accurate classification than existing clades but also shed light on the evolutionary trajectory of SARS-CoV-2.

BRIEFINGS IN BIOINFORMATICS (2021)

Review Public, Environmental & Occupational Health

The emergence and transmission of COVID-19 in European countries, 2019-2020: a comprehensive review of timelines, cases and containment

Waleed Al-Salem et al.

Summary: The study conducted a detailed analysis of the COVID-19 situation in European countries, finding that government non-pharmaceutical interventions successfully contained the rapid increase in cases. Heatmaps and maps were used to visualize the spread and impact of the pandemic. The research results help us better understand the transmission patterns and trends of the epidemic in Europe.

INTERNATIONAL HEALTH (2021)

Article Microbiology

Dating first cases of COVID-19

David L. Roberts et al.

Summary: The study suggests that COVID-19 may have emerged in China as early as November 17, 2019, and had spread globally by January 2020. Novel methods showed that six countries had exceptionally early cases, which were unlikely to be part of their main case series. These results imply an earlier and more rapid timeline of spread than previously thought based on confirmed cases.

PLOS PATHOGENS (2021)

Review Biochemical Research Methods

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Franziska Hufsky et al.

Summary: This review explores bioinformatics workflows and tools for the detection, analysis, tracking, evaluation, research, detection of drug targets, and development of therapeutic strategies related to SARS-CoV-2, providing valuable insights for the ongoing COVID-19 pandemic.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemical Research Methods

A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data

Shifu Chen et al.

Summary: This paper introduces a toolset and resources for rapid identification of viruses and microorganisms from sequencing data. Fastv is a lightweight tool that can detect microbial sequences, identify target microorganisms, and visualize coverage of microbial genomes. Experimental results show that fastv has achieved 100% sensitivity and 100% specificity in detecting SARS-CoV-2.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Oncology

Unexpected detection of SARS-CoV-2 antibodies in the prepandemic period in Italy

Giovanni Apolone et al.

Summary: The study found that the SARS-CoV-2 virus began circulating in Italy as early as September 2019 among asymptomatic individuals, shedding light on the origin and spread of the COVID-19 pandemic.

TUMORI JOURNAL (2021)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

Article Multidisciplinary Sciences

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou et al.

NATURE (2020)

Editorial Material Biochemistry & Molecular Biology

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

Yong-Zhen Zhang et al.

Review Dentistry, Oral Surgery & Medicine

Coronavirus Disease 19 (COVID-19): Implications for Clinical Dental Care

Amber Ather et al.

JOURNAL OF ENDODONTICS (2020)

Review Microbiology

Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses

Nicola Decaro et al.

VETERINARY MICROBIOLOGY (2020)

Article Medicine, Research & Experimental

Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant

Maria Pachetti et al.

JOURNAL OF TRANSLATIONAL MEDICINE (2020)

Article Biology

SARS-CoV-2 (COVID-19) by the numbers

Yinon M. Bar-On et al.

ELIFE (2020)

Article Microbiology

A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa

Romario Oliveira de Sales et al.

FRONTIERS IN MICROBIOLOGY (2020)

Review Genetics & Heredity

Phylogenetic tree building in the genomic age

Paschalia Kapli et al.

NATURE REVIEWS GENETICS (2020)

Article Microbiology

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Andrew Rambaut et al.

NATURE MICROBIOLOGY (2020)

Article Multidisciplinary Sciences

The impact of COVID-19 on small business outcomes and expectations

Alexander W. Bartik et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Surgery

The socio-economic implications of the coronavirus pandemic (COVID-19): A review

Maria Nicola et al.

INTERNATIONAL JOURNAL OF SURGERY (2020)

Article Biotechnology & Applied Microbiology

Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

Eva Wagner et al.

BMC GENOMICS (2020)

Article Infectious Diseases

SARS-CoV-2 and the human-animal interface: outbreaks on mink farms

Marion Koopmans

LANCET INFECTIOUS DISEASES (2020)

Article Virology

Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

Francesca Di Giallonardo et al.

VIRUSES-BASEL (2020)

Article Public, Environmental & Occupational Health

A One-Health approach for diagnosis and molecular characterization of SARS-CoV-2 in Italy

Alessio Lorusso et al.

ONE HEALTH (2020)

Article Infectious Diseases

Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP

Indrajit Saha et al.

INFECTION GENETICS AND EVOLUTION (2020)

Article Economics

Employment impact of Covid-19 crisis: from short term effects to long terms prospects

Marta Fana et al.

JOURNAL OF INDUSTRIAL AND BUSINESS ECONOMICS (2020)

Article Medicine, General & Internal

Acute respiratory distress syndrome

Michael A. Matthay et al.

NATURE REVIEWS DISEASE PRIMERS (2019)

Article Infectious Diseases

Development and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp.

Jagadesan Sankarasubramanian et al.

INFECTION GENETICS AND EVOLUTION (2019)

Article Microbiology

A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis

Bernd Neumann et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2019)

Article Biotechnology & Applied Microbiology

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Nathan D. Grubaugh et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

MLSTar: automatic multilocus sequence typing of bacterial genomes in R

Ignacio Ferres et al.

PEERJ (2018)

Article Biochemistry & Molecular Biology

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

Zhemin Zhou et al.

GENOME RESEARCH (2018)

Article Genetics & Heredity

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

Mickael Silva et al.

MICROBIAL GENOMICS (2018)

Editorial Material Infectious Diseases

GISAID: Global initiative on sharing all influenza data - from vision to reality

Yuelong Shu et al.

EUROSURVEILLANCE (2017)

Article Biochemical Research Methods

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

Heng Li

BIOINFORMATICS (2016)

Review Genetics & Heredity

Horizontal gene transfer: building the web of life

Shannon M. Soucy et al.

NATURE REVIEWS GENETICS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemical Research Methods

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Remco Bouckaert et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Genetics & Heredity

Molecular phylogenetics: principles and practice

Ziheng Yang et al.

NATURE REVIEWS GENETICS (2012)

Article Biochemistry & Molecular Biology

Dindel: Accurate indel calls from short-read data

Cornelis A. Albers et al.

GENOME RESEARCH (2011)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Virology

Viral Mutation Rates

Rafael Sanjuan et al.

JOURNAL OF VIROLOGY (2010)

Article Biochemistry & Molecular Biology

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

Kai Wang et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Microbiology

A new perspective on Listeria monocytogenes evolution

Marie Ragon et al.

PLOS PATHOGENS (2008)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2002)