Phylogenetic analysis

Last updated: 2021 Dec 15
Total hit(s): 17
Select item(s)
Key Findings
Comments
(You can add your comments too!)
Original Article
(hover to see details)
Phylogenetic analysis showed that all the Lambda variant isolates descended from a single ancestor, indicating monophyletic origin. The study also discovered that the Lambda variant with the deletion (RSYLTPGD246-253N) mutation first emerged around July 12, 2020 but was detected only on 8th November 2020 in Argentina. Through neutralisation assay, the study showed that the Lambda S is more resistant to the vaccine-induced antisera than the Lambda S derivative (Lambda+N246-253RSYLTPGD) which had recovered the RSYLTPGD246-253N deletion mutation. This supports the suggestion that the deletion mutation was a driving force behind the spread of the variant.
✍
 		Pre-print (bioRXiv)
Date of Publishing 2021 Jul 28
Title SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Impact factor
N/A
Date of Entry 2021 Dec 15

Phylogenetic analysis showed that by March 9 2021, all the SARS-CoV-2 Delta genomes discovered around the world had formed five distinct clusters: Delta1, Delta 2, pre-delta 3, Delta 3, and Delta 4. Since May 2021,Delta1 has gradually surpassed all other subvariants and emerged as the primary pandemic driver, with Delta 2 playing a minor role and the remaining two (delta 3 and delta 4) being inconsequential.
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Oct 20
Title SARS-COV-2 variant drives the pandemic in India and Europe via two subvariants
Impact factor
N/A
Date of Entry 2021 Nov 2

Phylogenetic analysis of 43 sequenced genomes identified 3 Pango lineages: SARS-CoV-2 Alpha (B.1.1.7), Kappa (B.1.617.1) and Delta (B.1.61.7.2) variants among the 146 flight passengers from New Delhi to Hong Kong in April 2021. Additional neighbouring cases could not be sequenced due to low viral load, and those cases could be missing links in the hypothesised transmission chains.
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Jul 23
Title Air travel-related outbreak of multiple SARS-CoV-2 variants
Impact factor
N/A
Date of Entry 2021 Nov 2

African viruses cluster closely with viruses from all continents, but especially with viruses from Europe, according to phylogenetic study. Only 143 of the 782 Pango lineages discovered around the world circulated in Africa, with five different lineages dominating at different times during the pandemic. The phylogenetic topological linkages revealed that African genomes tended to cluster with those from Europe, which is consistent with the continents' considerable cultural and commercial connectivity. Many notable outbreaks were foundin Egypt, the Democratic Republic of the Congo, Gambia, and South Africa, which reflects the greater number of sequences available in these countries.
✍
 		34031660
(medRxiv)
PMID
34031660
Date of Publishing: 2021 May 19
Title Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
Author(s) nameOkoh OS, Nii-Trebi NI et al.
Journal medRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Nov 2

In early 2021, routine genomic surveillance carried out in South Americadiscovered a deep-branching sublineage of Variant of Concern B.1.1.1, now known as Variant of Interest Lambda (C.37). Variants of Concern, on the other hand, were discovered less frequently in Peru over the first four months of 2021: Alpha, n=7, 0.5 percent; Gamma, n=17, 1.2 percent.
✍
 		Pre-print ( medRXiv )
Date of Publishing 2021 Jul 03
Title The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America
Impact factor
N/A
Date of Entry 2021 Sep 30

Phylogenetic analysis of 905 sequences showed that the introduction of the Alpha variant into Lebanon was via intermediate countries, rather than UK.
✍
 		Pre-print ( medRXiv )
Date of Publishing 2021 Aug 11
Title Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
Impact factor
N/A
Date of Entry 2021 Sep 30

M:I82T mutation was mostly present in 99.7% of B.1.525 lineage and 44% of B.1 lineages.
✍
 		tandfonline.com
Date of Publishing 2021 May 09
Title Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications
Impact factor
N/A
Date of Entry 2021 Sep 30

Phylogenetic analysis was performed for the RNA sequences from six patient samples which showed that they were infected with the Delta variant, despite being vaccinated. Out of 334 sequences analyzed, 328 were SARS-CoV-2 sequences designated for various variants of concern (VOC) and variant of interest (VOI), downloaded from GISAID, and 6 were the patient samples.
✍
 		Pre-print ( medRXiv )
Date of Publishing 2021 Jul 04
Title Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections
Impact factor
N/A
Date of Entry 2021 Aug 6

The emergent mutants L452R and Y453F had a wide range of hosts in terms of its receptor binding characteristics and participated in cross-species infection The cross-species transmission is a big threat to the pandemic.
✍
 		doi
Date of Publishing 2021 Apr 05
Title An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity
Impact factor
N/A
Date of Entry 2021 Aug 6

The most prevalent receptor binding motif (RBM) mutation N439K was subjected to phylogenetic analysis. N439K lineage i/B.1.141 was dominant in Scotland; while N439K lineage ii/B.1.258 were first sampled in Romania and currently spread to 32 other countries. The growth rate of N439K/D614G lineage(i) was similar compared to the N439/D614 or N439/D614G WT in Scotland. The total number of N439K variants as of January 6, 2021 correspond to 764,000 of the confirmed SARS-CoV-2 infections in 34 countries.
✍
 		33621484
(Cell)
PMID
33621484
Date of Publishing: 2021 Jan 28
Title Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Author(s) nameThomson EC, Rosen LE et al.
Journal Cell
Impact factor
27.35
Citation count: 259
Date of Entry 2021 Aug 6

Phylogenetic analysis of a sub-lineage of SARS-CoV-2 Alpha variant (B.1.1.7) showed that this lineage emerged through sequential acquisitions of mutation in the membrane (M:V70L) in November 2020 followed by the novel spike mutation (S:D178H) in February 2021. SARS-CoV-2 viral sequencing should be carried on a widespread scale to detect new mutations of concern.
✍
 		Pre-print ( medRXiv )
Date of Publishing 2021 May 18
Title Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations
Impact factor
N/A
Date of Entry 2021 Jul 2

The evolutionary tree analysis shows the sequential occurrence of characteristics mutations in the B.1.1.7 variant. The B.1.1.7 lineage belongs to the L1 subclade
✍
 		Pre-print ( bioRXiv )
Date of Publishing 2021 May 01
Title Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7
Impact factor
N/A
Date of Entry 2021 Jul 2

Phylogenetic analysis showed that the B.1.526 isolates can be branched into 3 sub-lineages, with 2 major lineages B.1.526-E484K and B.1.526-S477N containing A701V mutation and one smaller sub-lineage B.1.526-S477n containing Q957R mutation. Phylogenetic analyses of genomes containing a deletion (9bp deletion 106-108) in the non-spike region (ORF1a- nsp6) along with mutation A2262G clearly distinguishes the parent clade into B.1.526 variant and related viruses.
✍
 		Pre-print ( medRXiv )
Date of Publishing 2021 Apr 15
Title A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
Impact factor
N/A
Date of Entry 2021 Jul 2

The new VOI detected in 3 incoming travelers from Tanzania revealed identical genomes and presented highly divergent sequences within the A lineage (PANGO lineage B.1.351). These mutations are also present in other VOCs/VOIs like 501Y.V2/B.1.351, B.1.1.7, B.1.525 and C.16; and are suggested to be evolving under positive selection.
✍
 		Pre-print ( medRXiv )
Date of Publishing 2021 Apr 04
Title A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa
Impact factor
N/A
Date of Entry 2021 Jul 2

The phylogenetic analysis of the West Coast variants against the B.1.232 and B.1.243 lineages showed the mutations in S protein. The West Coast variants were differentiated by mutations at ORF1b:P976L(B.1.427) and ORF1a:I4205V(B.1.429). 1099 positive samples were derived from 12,124 tests.
✍
 		33688689
(medRxiv)
PMID
33688689
Date of Publishing: 2021 Mar 3
Title Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco
Author(s) namePeng J, Mann SA et al.
Journal medRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Jul 2

Phylogenetic studies showed the unusual accumulation of substitutions in the genome and relatively higher growth rate compared to other circulating lineages because of increased transmissibility(R) rather than shorter generation time Limitations : data analyzed did not entirely represent SARS-CoV-2 infections, the analysis was simple using parsimonious assumptions, the spatiotemporal correlation containing infectious disease data was not explicitly modelled.
✍
 		doi
Date of Publishing 2021 Jan 04
Title Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking B.1.1.7 in England: Insights from linking epidemiological and genetic data
Impact factor
N/A
Date of Entry 2021 Jul 2

Population genetic analysis and phylodynamic analysis using global SARS-CoV-2 phylogenies suggests that 614G increases in frequency relative to 614D in a way that suggests a selective advantage. No indication on higher COVID-19 mortality or clinical severity was observed but 614G variant is related to higher viral load and younger age of patients. Phylogenetic clusters of another variant, 614N, the independent origins of which suggest that this variant is also transmissible. There are only four other regions on the spike protein with 3 consecutive polymorphisms (S26, S846, S1228, and S1252) Limitation - selective advantage may also be due to a random founder effect.
✍
 		33275900
(Cell)
PMID
33275900
Date of Publishing: 2020 Nov 19
Title Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Author(s) nameVolz E, Hill V et al.
Journal Cell
Impact factor
27.35
Citation count: 412
Date of Entry 2021 Jul 2