Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values

L Duesterwald, M Nguyen, P Christensen, SW Long… - medRxiv, 2022 - medrxiv.org
The continuing emergence of SARS-CoV-2 variants of concern (VOCs) presents a serious
public health threat, exacerbating the effects of the COVID19 pandemic. Although millions of …

SARS-CoV-2 genome-based severity predictions correspond to lower qPCR values and higher viral load

M Skarzynski, EM McAuley, EJ Maier… - Global Health …, 2022 - cambridge.org
The 2019 coronavirus disease (COVID-19) pandemic has demonstrated the importance of
predicting, identifying, and tracking mutations throughout a pandemic event. As the COVID …

IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome

S Desai, A Rane, A Joshi, A Dutt - BMC bioinformatics, 2021 - Springer
Background Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in
surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and …

Phylogenomic early warning signals for SARS-CoV-2 epidemic waves

KO Drake, O Boyd, VB Franceschi, RM Colquhoun… - …, 2024 - thelancet.com
Background Epidemic waves of coronavirus disease 2019 (COVID-19) infections have often
been associated with the emergence of novel severe acute respiratory syndrome …

Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures

D Lebatteux, H Soudeyns, I Boucoiran, S Gantt… - Plos one, 2024 - journals.plos.org
Machine learning was shown to be effective at identifying distinctive genomic signatures
among viral sequences. These signatures are defined as pervasive motifs in the viral …

Enhanced deep convolutional neural network for sars-cov-2 variants classification

OI Awe, hesborn omwandho obura, MJ Mwanga… - bioRxiv, 2023 - biorxiv.org
High-throughput sequencing techniques and sequence analysis have enabled the
taxonomic classification of pathogens present in clinical samples. Sequencing provides an …

A multiplex PCR assay for identifying all major SARS-CoV-2 variants

RJ Dikdan, SAE Marras, AP Field, A Brownlee, A Cironi… - medRxiv, 2021 - medrxiv.org
Variants of Concern (VOC) of SARS-CoV-2, including Alpha, Beta, Gamma, and Delta,
threaten to prolong the pandemic leading to more global morbidity and mortality. Genome …

A multi-class gene classifier for SARS-CoV-2 variants based on convolutional neural network

J Fan, C Chen, C Song, J Pan, G Wu - bioRxiv, 2021 - biorxiv.org
Surveillance of circulating variants of severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) is of great importance in controlling the coronavirus disease 2019 (COVID …

Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

S Kubik, AC Marques, X Xing, J Silvery, C Bertelli… - bioRxiv, 2020 - biorxiv.org
Background SARS-CoV-2 genotyping has been instrumental to monitor virus evolution and
transmission during the pandemic. The reliability of the information extracted from the …

RCoV19: a one-stop hub for SARS-CoV-2 genome data integration, variant monitoring, and risk pre-warning

C Li, L Ma, D Zou, R Zhang, X Bai, L Li… - Genomics …, 2023 - academic.oup.com
Abstract The Resource for Coronavirus 2019 (RCoV19) is an open-access information
resource dedicated to providing valuable data on the genomes, mutations, and variants of …