Research graph
References from Genomic epidemiology of Omicron (BA.1) as a driver of Pakistan's fifth SARS-CoV-2 wave. Local targets link to admitted publications; unresolved targets remain external evidence.
Antibody evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2, and BA.3 sub-lineages
10.1016/j.chom.2022.05.001 · 2022 · External reference
Nextclade: clade assignment, mutation calling and quality control for viral genomes
10.21105/joss.03773 · 2021 · External reference
Unresolved reference
2022 · External reference
Unresolved reference
2010 · External reference
BEAGLE 3: improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics
10.1093/sysbio/syz020 · 2019 · External reference
Highperformance computing in Bayesian phylogenetics and phylodynamics using BEAGLE
10.1007/978-1-4939-9074-0_23 · 2019 · External reference
Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework
10.12688/wellcomeopenres.15770.1 · 2020 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
Global disparities in SARS-CoV-2 genomic surveillance
10.1038/s41467-022-33713-y · 2022 · External reference
Serum neutralization of SARS-CoV-2 Omicron sublineages BA.1 and BA.2 in patients receiving monoclonal antibodies
10.1038/s41591-022-01792-5 · 2022 · External reference
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Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization
10.1038/s41586-021-04387-1 · 2022 · External reference
A detailed overview of SARS-CoV-2 omicron: its sub-variants, mutations and pathophysiology, clinical characteristics, immunological landscape, immune escape, and therapies
10.3390/v15010167 · 2023 · External reference
Waning of BNT162b2 vaccine protection against SARS-CoV-2 infection in Qatar
10.1056/nejmoa2114114 · 2021 · External reference
Signals of significantly increased vaccine breakthrough, decreased hospitalization rates, and less severe disease in patients with coronavirus disease 2019 caused by the omicron variant of severe acute respiratory syndrome coronavirus 2 in Houston, Texas
10.1016/j.ajpath.2022.01.007 · 2022 · External reference
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Omicron variant (B.1.1.529) and its sublineages: what do we know so far amid the emergence of recombinant variants of SARS-CoV-2?
10.1016/j.biopha.2022.113522 · 2022 · External reference
Relaxed phylogenetics and dating with confidence
10.1371/journal.pbio.0040088 · 2006 · External reference
Unresolved reference
2021 · External reference
Twin peaks: the omicron SARS-CoV-2 Ba. 1 and Ba. 2 epidemics in England
10.1126/science.abq4411 · 2022 · External reference
Neutralization of SARS-CoV2 Omicron sub-lineages BA.1, BA.1.1, and BA.2
10.1016/j.chom.2022.04.014 · 2022 · External reference
Emergence of within-host SARS-CoV-2 recombinant genome after coinfection by gamma and delta variants: a case report
10.3389/fpubh.2022.849978 · 2022 · External reference
Outbreak. Info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
10.1038/s41592-023-01769-3 · 2023 · External reference
Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci
10.1093/molbev/mss265 · 2013 · External reference
Breakthrough SARS-CoV-2 infections during periods of delta and omicron predominance, South Africa
10.1016/s0140-6736(22)01190-4 · 2022 · External reference
Nextstrain: real-time tracking of pathogen evolution
10.1093/bioinformatics/bty407 · 2018 · External reference
Mitigating Covid-19 in the face of emerging virus variants, breakthrough infections and vaccine hesitancy
10.1016/j.jaut.2021.102792 · 2022 · External reference
SARS-CoV-2 variants, spike mutations and immune escape
10.1038/s41579-021-00573-0 · 2021 · External reference
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
10.1007/bf02101694 · 1985 · External reference
In search of covariates of HIV-1 subtype B spread in the United States—a cautionary tale of large-scale Bayesian phylogeography
10.3390/v12020182 · 2020 · External reference
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
10.21105/joss.02906 · 2021 · External reference
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Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events
10.1038/s41392-022-00992-2 · 2022 · External reference
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
10.1093/nar/gkf436 · 2002 · External reference
COVID-19 vaccine–long term immune decline and breakthrough infections
10.1016/j.vaccine.2021.10.038 · 2021 · External reference
Unresolved reference
2026 · External reference
Impact and mitigation of sampling bias to determine viral spread: evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations
10.1093/ve/vead010 · 2023 · External reference
Bayesian phylogeography finds its roots
10.1371/journal.pcbi.1000520 · 2009 · External reference
Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2
10.1038/s41467-020-18877-9 · 2020 · External reference
Monitoring of the SARS-CoV2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases
10.1016/j.medj.2022.07.007 · 2022 · External reference
Waning immune humoral response to BNT162b2 Covid-19 vaccine over 6 months
10.1056/nejmoa2114583 · 2021 · External reference
Fast and accurate long-read alignment with Burrows–Wheeler transform
10.1093/bioinformatics/btp698 · 2010 · External reference
Lineage ba. 2 dominated the omicron SARS-CoV-2 epidemic wave in the Philippines
10.1093/ve/veac078 · 2022 · External reference
The P681H mutation in the spike glycoprotein of the alpha variant of SARS-CoV-2 escapes IFITM restriction and is necessary for type I interferon resistance
10.1128/jvi.01250-22 · 2022 · External reference
Household transmission of SARS-CoV-2 omicron variant of concern subvariants Ba. 1 and Ba. 2 in Denmark
2022 · External reference
Unresolved reference
2022 · External reference
Covid-19: what do we know about omicron sublineages?
2022 · External reference
Unresolved reference
2022 · External reference
The evolution of SARS-CoV-2
10.1038/s41579-023-00878-2 · 2023 · External reference
The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants
10.1038/s41598-022-21564-y · 2022 · External reference
IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
10.1093/molbev/msaa015 · 2020 · External reference
Twin combination of Omicron and Delta variants triggering a tsunami wave of ever high surges in COVID-19 cases: a challenging global threat with a special focus on the Indian subcontinent
10.1002/jmv.27585 · 2022 · External reference
Omicron (B.1.1.529 variant of SARS-CoV-2); an emerging threat: current global scenario
10.1002/jmv.27561 · 2022 · External reference
Evolutionary history and introduction of SARS-CoV-2 alpha VOC/B.1.1.7 in Pakistan through international travelers
10.1093/ve/veac020 · 2022 · External reference
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
10.1093/molbev/msu300 · 2015 · External reference
Omicron SARS-CoV-2 variant spike protein shows an increased affinity to the human ACE2 receptor: an in silico analysis
10.3390/pathogens11010045 · 2021 · External reference
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
10.1093/ve/veab064 · 2021 · External reference
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Rapid, sensitive, full-genome sequencing of severe acute respiratory syndrome coronavirus 2
10.3201/eid2610.201800 · 2020 · External reference
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Effects of BA.1/BA.2 subvariant, vaccination and prior infection on infectiousness of SARS-CoV-2 Omicron infections
10.1093/jtm/taac068 · 2022 · External reference
Unresolved reference
2020 · External reference
The omicron subvariant ba. 2: birth of a new challenge during the COVID-19 pandemic
10.1016/j.ijsu.2022.106261 · 2022 · External reference
Posterior summarization in Bayesian phylogenetics using tracer 1.7
10.1093/sysbio/syy032 · 2018 · External reference
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
10.1038/s41564-020-0770-5 · 2020 · External reference
Unresolved reference
2020 · External reference
Mathematical assessment of the role of waning and boosting immunity against the BA.1 omicron variant in the United States
10.3934/mbe.2023009 · 2023 · External reference
TreeTime: maximum-likelihood phylodynamic analysis
10.1093/ve/vex042 · 2018 · External reference
Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation
10.1038/s41586-021-04266-9 · 2022 · External reference
Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant
10.1186/s12916-022-02312-5 · 2022 · External reference
Unresolved reference
2022 · External reference
GISAID: global initiative on sharing all influenza data–from vision to reality
10.2807/1560-7917.es.2017.22.13.30494 · 2017 · External reference
Some probabilistic and statistical problems on the analysis of DNA sequence
1986 · External reference
The influence of rate heterogeneity among sites on the time dependence of molecular rates
10.1093/molbev/mss140 · 2012 · External reference
SARS-CoV-2 vaccination and the bridge between first and fourth dose: where are we?
10.3390/vaccines10030444 · 2022 · External reference
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
10.1093/ve/vey016 · 2018 · External reference
The biological and clinical significance of emerging SARS-CoV-2 variants
10.1038/s41576-021-00408-x · 2021 · External reference
Unresolved reference
2022 · External reference
Unresolved reference
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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
10.1038/s41586-022-04411-y · 2022 · External reference
Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study
10.1016/s0140-6736(22)00017-4 · 2022 · External reference
Virological characteristics of the SARS-CoV-2 Omicron BA. 2 spike
10.1016/j.cell.2022.04.035 · 2022 · External reference
Estimating the pattern of nucleotide substitution
10.1007/bf00178256 · 1994 · External reference
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
10.1007/bf00160154 · 1994 · External reference
A space-time process model for the evolution of DNA sequences
10.1093/genetics/139.2.993 · 1995 · External reference
Omicron ba. 2 lineage predominance in severe acute respiratory syndrome coronavirus 2 positive cases during the third wave in North India
10.3389/fmed.2022.955930 · 2022 · External reference
Estimation of evolutionary distances between nucleotide sequences
10.1007/bf00160155 · 1994 · External reference
