Genomic data support multiple introductions and explosive demographic expansions in a highly invasive aquatic insect

Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

Download Full-text

Detection of SARS-CoV-2 variant 501Y.V2 in Comoros Islands in January 2021

Wellcome Open Research ◽

10.12688/wellcomeopenres.16889.1 ◽

2021 ◽

Vol 6 ◽

pp. 192

Author(s):

Charles N. Agoti ◽

George Githinji ◽

Khadija S. Mohammed ◽

Arnold W. Lambisia ◽

Zaydah R. de Laurent ◽

...

Keyword(s):

Common Ancestor ◽

Control Strategies ◽

Close Association ◽

Genomic Data ◽

Recent Common Ancestor ◽

Major Infection ◽

Multiple Introductions ◽

Most Recent Common Ancestor ◽

The Indian Ocean ◽

Local Transmission

Background. Genomic data is key in understanding the spread and evolution of SARS-CoV-2 pandemic and informing the design and evaluation of interventions. However, SARS-CoV-2 genomic data remains scarce across Africa, with no reports yet from the Indian Ocean islands. Methods. We genome sequenced six SARS-CoV-2 positive samples from the first major infection wave in the Union of Comoros in January 2021 and undertook detailed phylogenetic analysis. Results. All the recovered six genomes classified within the 501Y.V2 variant of concern (also known as lineage B.1.351) and appeared to be from 2 sub-clusters with the most recent common ancestor dated 30th Oct-2020 (95% Credibility Interval: 06th Sep-2020 to 10th Dec-2020). Comparison of the Comoros genomes with those of 501Y.V2 variant of concern from other countries deposited into the GISAID database revealed their close association with viruses identified in France and Mayotte (part of the Comoros archipelago and a France, Overseas Department). Conclusions. The recovered genomes, albeit few, confirmed local transmission following probably multiple introductions of the SARS-CoV-2 501Y.V2 variant of concern during the Comoros’s first major COVID-19 wave. These findings demonstrate the importance of genomic surveillance and have implications for ongoing control strategies on the islands.

Download Full-text

Genomic Data Support the Elevation of the Federally Listed El Segundo Blue (Euphilotes bernardino/Battoides allyni) to Species Status

Journal of the Lepidopterists’ Society ◽

10.18473/lepi.75i2.a10 ◽

2021 ◽

Vol 75 (2) ◽

Author(s):

Daniel Rubinoff ◽

Travis Longcore ◽

Julian R. Dupuis ◽

Kendall H. Osborne

Keyword(s):

Genomic Data ◽

Species Status ◽

Data Support

Download Full-text

Integrated genomic view of SARS-CoV-2 in India

10.1101/2020.06.04.128751 ◽

2020 ◽

Cited By ~ 2

Author(s):

Pramod Kumar ◽

Rajesh Pandey ◽

Pooja Sharma ◽

Mahesh S Dhar ◽

A Vivekanand ◽

...

Keyword(s):

Real Time ◽

Host Response ◽

Genomic Data ◽

Amplicon Sequencing ◽

Climatic Conditions ◽

Therapeutic Interventions ◽

Molecular Surveillance ◽

Multiple Introductions ◽

Oxford Nanopore ◽

Local Transmission

SUMMARYIndia first detected SARS-CoV-2, causal agent of COVID-19 in late January-2020, imported from Wuhan, China. March-2020 onwards; importation of cases from rest of the countries followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT from Oxford Nanopore Technology to understand introduction and local transmission. The analyses revealed multiple introductions of SARS-CoV-2 from Europe and Asia following local transmission. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, here, proposed as A4-clade based on its divergence within A-cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Despite the effectiveness of non-therapeutic interventions in India, multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

Download Full-text

Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0407270101 ◽

2004 ◽

Vol 101 (49) ◽

pp. 17021-17026 ◽

Cited By ~ 87

Author(s):

M. E. Steiper ◽

N. M. Young ◽

T. Y. Sukarna

Keyword(s):

Genomic Data ◽

Early Oligocene ◽

Data Support

Download Full-text

Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa

BMC Genomics ◽

10.1186/s12864-021-07870-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wasfi Fares ◽

Anissa Chouikha ◽

Kais Ghedira ◽

Meriam Gdoura ◽

Dorra Rezig ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

North Africa ◽

Vaccine Development ◽

Genomic Data ◽

Whole Genome ◽

International Level ◽

Multiple Introductions ◽

Nucleotide Divergence ◽

Preliminary Study

Abstract Background In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses circulating in Tunisia and worldwide. Methods Whole genome sequencing was performed using NGS approach on six SARS. CoV-2 highly positive samples detected during the early phase of the outbreak. Results Full genomes sequences of six Tunisian SARS-CoV-2 strains were obtained from imported and locally transmission cases during the COVID-19 outbreak. Reported sequences were non-identical with 0.1% nucleotide divergence rate and clustered into 6 different clades with worldwide sequences. SNPs results favor the distribution of the reported Tunisian sequences into 3 major genotypes. These SNP mutations are critical for diagnosis and vaccine development. Conclusions These results indicate multiple introductions of the virus in Tunisia and add new genomic data on SARS-CoV-2 at the international level.

Download Full-text

Discrimination of monomer from multimer DNA disk-shaped toruses by freezeetch TEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100111161 ◽

1984 ◽

Vol 42 ◽

pp. 210-211

Author(s):

George C. Ruben ◽

Kenneth A. Marx

Keyword(s):

Biochemical Data ◽

Dna Structures ◽

Ice Surface ◽

Double Stranded Dna ◽

Data Support ◽

Dna Organization ◽

Trivalent Cations

In vitro collapse of DNA by trivalent cations like spermidine produces torus (donut) shaped DNA structures thought to have a DNA organization similar to certain double stranded DNA bacteriophage and viruses. This has prompted our studies of these structures using freeze-etch low Pt-C metal (9Å) replica TEM. With a variety of DNAs the TEM and biochemical data support a circumferential DNA winding model for hydrated DNA torus organization. Since toruses are almost invariably oriented nearly horizontal to the ice surface one of the most accessible parameters of a torus population is annulus (ring) thickness. We have tabulated this parameter for populations of both nicked, circular (Fig. 1: n=63) and linear (n=40: data not shown) ϕX-174 DNA toruses. In both cases, as can be noted in Fig. 1, there appears to be a compact grouping of toruses possessing smaller dimensions separated from a dispersed population possessing considerably larger dimensions.

Download Full-text