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

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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Assessment of Metagenomic MinION and Illumina sequencing as an approach for the recovery of whole genome sequences of chikungunya and dengue viruses directly from clinical samples

10.1101/355560 ◽

2018 ◽

Cited By ~ 2

Author(s):

Liana E. Kafetzopoulou ◽

Kyriakos Efthymiadis ◽

Kuiama Lewandowski ◽

Ant Crook ◽

Dan Carter ◽

...

Keyword(s):

Dengue Virus ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Illumina Miseq ◽

Clinical Samples ◽

Whole Genome ◽

Metagenomic Sequencing ◽

Front Line ◽

Genome Sequences ◽

Oxford Nanopore

AbstractThe recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. We performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION to study the feasibility of whole genome sequencing from clinical samples containing chikungunya or dengue virus, two of the most important arboviruses. Direct metagenomic sequencing of nucleic acid extracts from serum and plasma without viral enrichment allowed for virus and coinfection identification, subtype determination and in the majority of cases elucidated complete or near-complete genomes adequate for phylogenetic analysis. This work demonstrates that metagenomic whole genome sequencing is feasible for over 90% and 80% of chikungunya and dengue virus PCR-positive patient samples respectively. It confirms the feasibility of field metagenomic sequencing for these and likely other RNA viruses, highlighting the applicability of this approach to front-line public health.

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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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Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical Samples

Genome Announcements ◽

10.1128/genomea.01462-15 ◽

2015 ◽

Vol 3 (6) ◽

Cited By ~ 4

Author(s):

Ainsley C. Nicholson ◽

Melissa Bell ◽

Ben W. Humrighouse ◽

John R. McQuiston

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Clinical Relevance ◽

Complete Genome ◽

Growth Characteristics ◽

Clinical Samples ◽

Whole Genome ◽

The Novel ◽

Genome Sequences ◽

Gram Positive

Here we report the complete genome sequences of two strains of the novel fastidious, partially acid-fast, Gram-positive bacillus “ Lawsonella clevelandensis ” (proposed). Their clinical relevance and unusual growth characteristics make them intriguing candidates for whole-genome sequencing.

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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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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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Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia

BMC Genomics ◽

10.1186/s12864-019-6400-z ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 1

Author(s):

Everlyn Kamau ◽

John W. Oketch ◽

Zaydah R. de Laurent ◽

My V. T. Phan ◽

Charles N. Agoti ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Stop Codon ◽

Amino Acid Level ◽

Respiratory Illness ◽

Human Metapneumovirus ◽

Clinical Samples ◽

Whole Genome ◽

Individual Gene

Abstract Background Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. Results We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. Conclusion This is the first genomic characterization of HMPV genomes from African patients.

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Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

BMC Veterinary Research ◽

10.1186/s12917-021-02945-3 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Jacqueline King ◽

Anne Pohlmann ◽

Kamila Dziadek ◽

Martin Beer ◽

Kerstin Wernike

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Economic Losses ◽

Clinical Samples ◽

Bovine Viral Diarrhea ◽

Sequence Information ◽

Whole Genome ◽

Diarrhea Virus ◽

Viral Diarrhea ◽

Viral Loads

Abstract Background As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genetically differentiated into 21 BVDV-1 and four BVDV-2 subtypes. Commonly, the 5’ untranslated region and the Npro protein are utilized for subtyping. However, the genetic variability of BVDV leads to limitations in former studies analyzing genome fragments in comparison to a full-genome evaluation. Results To enable rapid and accessible whole-genome sequencing of both BVDV-1 and BVDV-2 strains, nanopore sequencing of twelve representative BVDV samples was performed on amplicons derived through a tiling PCR procedure. Covering a multitude of subtypes (1b, 1d, 1f, 2a, 2c), sample matrices (plasma, EDTA blood and ear notch), viral loads (Cq-values 19–32) and species (cattle and sheep), ten of the twelve samples produced whole genomes, with two low titre samples presenting 96 % genome coverage. Conclusions Further phylogenetic analysis of the novel sequences emphasizes the necessity of whole-genome sequencing to identify novel strains and supplement lacking sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive and accessible obtainment of complete BVDV genomes.

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Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India

Genome Announcements ◽

10.1128/genomea.00598-17 ◽

2017 ◽

Vol 5 (28) ◽

Cited By ~ 1

Author(s):

Sara Jones ◽

Raji Prasad ◽

Anjana S. Nair ◽

Sanjai Dharmaseelan ◽

Remya Usha ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Analysis ◽

Influenza A ◽

Whole Genome Sequence ◽

Whole Genome ◽

H1n1 Pandemic ◽

Genome Sequences ◽

Influenza A H1n1 ◽

Virus Isolates ◽

New Mutations

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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Advancing RNA Virus Discovery and Biology with Whole Genome Sequencing

10.21007/etd.cghs.2021.0551 ◽

2021 ◽

Author(s):

◽

Mariah Taylor ◽

Keyword(s):

Genetic Variation ◽

Amino Acid ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rna Virus ◽

Animal Health ◽

Functional Domains ◽

Whole Genome ◽

Coding Region

Two RNA virus families that pose a threat to human and animal health are Hantaviridae and Coronaviridae. These RNA viruses which originate in wildlife continue and will continue to cause disease, and hence, it is critical that scientific research define the mechanisms as to how these viruses spillover and adapt to new hosts to become endemic. One gap in our ability to define these mechanisms is the lack of whole genome sequences for many of these viruses. To address this specific gap, I developed a versatile amplicon-based whole-genome sequencing (WGS) approach to identify viral genomes of hantaviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within reservoir and spillover hosts. In my research studies, I used the amplicon-based WGS approach to define the genetic plasticity of viral RNA within pathogenic and nonpathogenic hantavirus species. The standing genetic variation of Andes orthohantavirus and Prospect Hill orthohantavirus was mapped out and amino acid changes occurring outside of functional domains were identified within the nucleocapsid and glycoprotein. I observed several amino acid changes in functional domains of the RNA-dependent RNA polymerase, as well as single nucleotide polymorphisms (SNPs) within the 3’ non-coding region (NCR) of the S-segment. To identify whether virus adaptation would occur within the S- and L-segments we attempted to adapt hantaviruses in vitro in a spillover host model through passaging experiments. In early passages we identified few mutations in the M-segment with the majority being identified in the S-segment 3’ NCR and the L-segment. This work suggests that hantavirus adaptation occurs in the S- and L-segments although the effect of these mutants on pathology is yet to be determined. While sequencing laboratory isolates is easily accomplished, sequencing low concentrations of virus within the reservoir is a formidable task. I further translated our amplicon-based WGS approach into a pan-oligonucleotide amplicon-based WGS approach to sequence hantavirus vRNA and mRNA from reservoir and spillover hosts in Ukraine. This approach successfully identified a novel Puumala orthohantavirus (PUUV) strain in Ukraine and using Bayesian phylogenetics we found this strain to be associated with the PUUV Latvian lineage. Early during the SARS-CoV-2 pandemic, I applied the knowledge gained in the hantavirus WGS efforts to sequencing of SARS-CoV-2 from nasopharyngeal swabs collected in April 2020. The genetic diversity of 45 SARS-CoV-2 isolates was evaluated with the methods I developed. We identified D614G, a notable mutation known for increasing transmission, in over 90% of our isolates. Two major lineages distinguish SARS-CoV-2 variants worldwide, lineages A and B. While most of our isolates were found within B lineage, we also identified one isolate within lineage A. We performed in vitro work which confirmed A lineage isolates as having poor replication in the trachea as compared to the nasal cavity. Five of these isolates presented a unique array of mutations which were assessed in the keratin 18 human angiotensin-converting enzyme 2 (K18-hACE2) mouse model for its response immunologically and pathogenically. We identified a distinction of pathogenesis between the A and B lineages with emphysema being common amongst A lineage isolates. Additionally, we discovered a small cohort of likely SNPs that defined the late induction of eosinophils during infection. In summary, this work will further define the dynamics of genetic variation and plasticity within virus populations that cause disease outbreaks and will allow a deeper understanding of the virus-host relationship.

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