[HTML][HTML] HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
PT Truong Nguyen, I Plyusnin, T Sironen… - BMC …, 2021 - Springer
Background SARS-CoV-2 related research has increased in importance worldwide since
December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the …
December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the …
ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time
Motivation The ongoing evolution of SARS-CoV-2 and the rapid emergence of variants of
concern at distinct geographic locations have relevant implications for the implementation of …
concern at distinct geographic locations have relevant implications for the implementation of …
[HTML][HTML] Stability of SARS-CoV-2 phylogenies
The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due
to the rapid community sequencing response. Researchers immediately leveraged these …
to the rapid community sequencing response. Researchers immediately leveraged these …
[PDF][PDF] Nextclade: clade assignment, mutation calling and quality control for viral genomes
The variants of concern (VoCs) of SARS-CoV-2 have highlighted the need for a global
molecular surveillance of pathogens via whole genome sequencing. Such sequencing, for …
molecular surveillance of pathogens via whole genome sequencing. Such sequencing, for …
[HTML][HTML] Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation
ZS Wallace, J Davis, AM Niewiadomska… - Frontiers in …, 2022 - frontiersin.org
Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has demonstrated its ability to
rapidly and continuously evolve, leading to the emergence of thousands of different …
rapidly and continuously evolve, leading to the emergence of thousands of different …
The genomic variation landscape of globally-circulating clades of SARS-CoV-2 defines a genetic barcoding scheme
We describe fifteen major mutation events from 2,058 high-quality SARS-CoV-2 genomes
deposited up to March 31st, 2020. These events define five major clades (G, I, S, D and V) of …
deposited up to March 31st, 2020. These events define five major clades (G, I, S, D and V) of …
[HTML][HTML] Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples
S Kubik, AC Marques, X Xing, J Silvery… - Clinical Microbiology …, 2021 - Elsevier
Objectives Genotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
has been instrumental in monitoring viral evolution and transmission during the pandemic …
has been instrumental in monitoring viral evolution and transmission during the pandemic …
[HTML][HTML] Emergence of novel SARS-CoV-2 variants in the Netherlands
Abstract Coronavirus disease 2019 (COVID-19) has emerged in December 2019 when the
first case was reported in Wuhan, China and turned into a pandemic with 27 million …
first case was reported in Wuhan, China and turned into a pandemic with 27 million …
COV2Var, a function annotation database of SARS-CoV-2 genetic variation
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss
of millions of lives and severe global economic consequences. Every time SARS-CoV-2 …
of millions of lives and severe global economic consequences. Every time SARS-CoV-2 …
[HTML][HTML] Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays
An epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing
coronavirus diseases (C0VID-19) initially reported in Wuhan, China has rapidly emerged …
coronavirus diseases (C0VID-19) initially reported in Wuhan, China has rapidly emerged …
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