First whole genome sequences and phylogenetic analysis of SARS-CoV-2 virus isolates during COVID-19 outbreak in Tunisia, North Africa.

ABSTRACT We report here the whole-genome sequence of six clinical isolates of influenza A(H1N1)pdm09, isolated from Kerala, India. Amino acid analysis of all gene segments from the A(H1N1)pdm09 isolates obtained in 2014 and 2015 identified several new mutations compared to the 2009 A(H1N1) pandemic strain.

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Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽

10.3390/genes12111803 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1803

Author(s):

Jitendra Singh ◽

Anvita Gupta Malhotra ◽

Debasis Biswas ◽

Prem Shankar ◽

Leena Lokhande ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Spike Protein ◽

Whole Genome ◽

The Novel ◽

Genome Sequences ◽

Second Wave ◽

Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

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Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations

Virus Evolution ◽

10.1093/ve/veaa018 ◽

2020 ◽

Vol 6 (1) ◽

Cited By ~ 4

Author(s):

Artem Baidaliuk ◽

Sébastian Lequime ◽

Isabelle Moltini-Conclois ◽

Stéphanie Dabo ◽

Laura B Dickson ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Aedes Aegypti ◽

Evolutionary History ◽

Host Population ◽

Viral Metagenomics ◽

Insect Host ◽

Genome Sequences ◽

Geographical Clustering ◽

Virus Isolates

Abstract Flaviviruses encompass not only medically relevant arthropod-borne viruses (arboviruses) but also insect-specific flaviviruses (ISFs) that are presumably maintained primarily through vertical transmission in the insect host. Interestingly, ISFs are commonly found infecting important arbovirus vectors such as the mosquito Aedes aegypti. Cell-fusing agent virus (CFAV) was the first described ISF of mosquitoes more than four decades ago. Despite evidence for widespread CFAV infections in A.aegypti populations and for CFAV potential to interfere with arbovirus transmission, little is known about CFAV evolutionary history. Here, we generated six novel CFAV genome sequences by sequencing three new virus isolates and subjecting three mosquito samples to untargeted viral metagenomics. We used these new genome sequences together with published ones to perform a global phylogenetic analysis of CFAV genetic diversity. Although there was some degree of geographical clustering among CFAV sequences, there were also notable discrepancies between geography and phylogeny. In particular, CFAV sequences from Cambodia and Thailand diverged significantly, despite confirmation that A.aegypti populations from both locations are genetically close. The apparent phylogenetic discrepancy between CFAV and its A.aegypti host in Southeast Asia indicates that other factors than host population structure shape CFAV genetic diversity.

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Complete Genome Sequences of 11 Newcastle Disease Virus Isolates of Subgenotype VII.2 from Indonesia

Microbiology Resource Announcements ◽

10.1128/mra.01519-19 ◽

2020 ◽

Vol 9 (5) ◽

Author(s):

Iryna V. Goraichuk ◽

Dawn Williams-Coplin ◽

Michael H. Wibowo ◽

Peter A. Durr ◽

Widya Asmara ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Newcastle Disease Virus ◽

Disease Virus ◽

Newcastle Disease ◽

Complete Genome ◽

Class Ii ◽

Genome Sequences ◽

Layer Chickens ◽

Virus Isolates

We report the complete genome sequences of 11 virulent Newcastle disease viruses. The isolates were obtained from vaccinated broiler and layer chickens in three different provinces of Indonesia in 2013 and 2014. Phylogenetic analysis revealed that all isolates belong to subgenotype VII.2 in the class II cluster.

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Novel characteristics of Chinese NADC34-like PRRRSV during 2020-2021

10.22541/au.164052227.77640850/v1 ◽

2021 ◽

Author(s):

Hu Xu ◽

Chao Li ◽

Wansheng Li ◽

Jing Zhao ◽

Bangjun Gong ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Genome Sequencing ◽

Clinical Samples ◽

Whole Genome ◽

Recombination Analysis ◽

Genome Sequences ◽

First Time ◽

Additional Amino Acid ◽

Independent Branch

NADC34-like PRRSV strains were first detected in China in 2017, with epidemic potential. In this study, the phylogenetic, epidemic, and recombinant properties of NADC34-like PRRSV in China were evaluated comprehensively. From 2020 to October 2021, 82 NADC34-like PRRSV isolates were obtained from 433 PRRSV-positive clinical samples. These strains accounted for 11.5% and 28.6% of positives in 2020 and 2021, respectively, and have spread to eight provinces. We selected 15 samples for whole-genome sequencing, revealing genome lengths of 15,009 to 15,113 nt. Phylogenetic analysis revealed that Chinese NADC34-like strains cluster with American sublineage 1.5 strains and do not form an independent branch. Recombination analysis revealed that six of fifteen complete genome sequences derived from recombination between NADC34-like and NADC30-like or HP-PRRSV; they all recombined with local strains in China, exhibiting a complex recombination pattern. Partial Nsp2 sequence alignment showed that nine of fifteen isolates have a continuous 100-aa deletion (similar to IA/2014/NADC34); other isolates have a 131-aa discontinuity deletion (similar to NADC30). Five of them also have additional amino acid deletions, all of which are reported for the first time here. In the last two years, NADC34-like PRRSV has become one of the main epidemic strains in some areas of China; it has changed significantly, its homology has decreased significantly, and it has undergone complex recombination with local Chinese strains. These results are of great significance for understanding the current epidemic situation of PRRSV in China.

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Molecular Characterization of Invasive Isolates ofNeisseria meningitidisin Casablanca, Morocco

Journal of Clinical Microbiology ◽

10.1128/jcm.00445-18 ◽

2018 ◽

Vol 56 (7) ◽

Cited By ~ 3

Author(s):

Aziza Razki ◽

Eva Hong ◽

Khalid Zerouali ◽

Houria Belabbes ◽

Khadija Aitmouss ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genome Sequencing ◽

North Africa ◽

Clonal Complex ◽

Sequence Type ◽

Whole Genome ◽

Content Type ◽

Vaccination Strategies ◽

Few Data

ABSTRACTMeningococcal epidemiology may change unpredictably, and typing ofNeisseria meningitidisisolates is crucial for the surveillance of invasive meningococcal disease (IMD). Few data are available regarding the meningococcal epidemiology in countries of North Africa. We aimed to explore invasive meningococcal isolates from the Casablanca region in Morocco. We used whole-genome sequencing (WGS) to characterize 105 isolates from this region during the period of 2011 to 2016. Our data showed that the majority (n= 100) of the isolates belonged to serogroup B. Genotyping indicated that most of the isolates (n= 62) belonged to sequence type 33 of clonal complex 32. The isolates also showed the same PorA and FetA markers and clustered together on the basis of WGS phylogenetic analysis; they seemed to correspond to an expansion of local isolates in the Casablanca region, as reported for similar isolates in several other countries. These data suggest that serogroup B isolates may predominate in Morocco, which may have an important impact in the design of vaccination strategies.

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First phylogenetic analysis of Malian SARS-CoV-2 sequences provide molecular insights into the genomic diversity of the Sahel region

10.1101/2020.09.23.20165639 ◽

2020 ◽

Author(s):

Bourema Kouriba ◽

Angela Duerr ◽

Alexandra Rehn ◽

Abdoul Karim Sangare ◽

Brehima Youssouf Traoure ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genome Sequencing ◽

Sequence Data ◽

Genomic Diversity ◽

Whole Genome ◽

Sequencing Data ◽

Genome Sequences ◽

Spreading Dynamics ◽

Sahel Region ◽

Limited Sequence

We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occuring in the Wuhan region, China, in December 2019. From China the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on the 2nd of March 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequence data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening of 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates from which 21 whole genome sequences were generated. Our analysis shows that both, the early A (19B) and the fast evolving B (20A/C) clade, are present in Mali indicating multiple and independent introductions of the SARS-CoV-2 to the Sahel region.

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Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates

Archives of Virology ◽

10.1007/s00705-019-04437-0 ◽

2019 ◽

Vol 165 (1) ◽

pp. 21-31 ◽

Cited By ~ 1

Author(s):

A. M. Dullemans ◽

M. Botermans ◽

M. J. D. de Kock ◽

C. E. de Krom ◽

T. A. J. van der Lee ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Complete Genome ◽

New Genus ◽

Sequence Data ◽

Amino Acid Sequences ◽

Ringspot Virus ◽

Genome Sequences ◽

The Family ◽

Virus Isolates

Abstract To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

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First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region

Viruses ◽

10.3390/v12111251 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1251

Author(s):

Bourema Kouriba ◽

Angela Dürr ◽

Alexandra Rehn ◽

Abdoul Karim Sangaré ◽

Brehima Y. Traoré ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Diversity ◽

Whole Genome ◽

Sequencing Data ◽

Genome Sequences ◽

Spreading Dynamics ◽

Sahel Region

We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on 2 March 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequencing data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates, from which 21 whole genome sequences were generated. Our analysis shows that both the early A (19B) and the later observed B (20A/C) clade are present in Mali, indicating multiple and independent introductions of SARS-CoV-2 to the Sahel region.

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Full-Genome Sequences of Seven Fatal Enterovirus 71 Strains Isolated in Shenzhen, China, in 2014: TABLE 1

Genome Announcements ◽

10.1128/genomea.00316-16 ◽

2016 ◽

Vol 4 (2) ◽

Cited By ~ 2

Author(s):

Long Chen ◽

Ya-Qing He ◽

Jun Meng ◽

Ling-Hong Xiong ◽

Chao Wang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Complete Genome ◽

Close Relationships ◽

Southern China ◽

Enterovirus 71 ◽

Whole Genome ◽

Vp1 Gene ◽

Full Genome ◽

Genome Sequences

The whole-genome sequences of seven fatal enterovirus 71 (EV71) strains, isolated in southern China, in 2014, were determined. The complete genome sequences of these strains displayed close relationships to native EV71 strains and showed 94.2% to 99.8% identity to each other. All of these strains were assigned to subgenotype C4a based on phylogenetic analysis of the VP1 gene.

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