scholarly journals Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7

2021 ◽  
Vol 9 (4) ◽  
pp. 748
Author(s):  
Marek Widera ◽  
Barbara Mühlemann ◽  
Victor M. Corman ◽  
Tuna Toptan ◽  
Jörn Beheim-Schwarzbach ◽  
...  
Keyword(s):  
Protein S ◽  
International Travel ◽  
Full Genome Sequence ◽  
Nasopharyngeal Swab ◽  
Full Genome ◽  
Viral Sequence ◽  
Amino Acid Deletion ◽  
Full Genome Sequencing ◽  
Frankfurt Am Main ◽  
The City

Background: International travel is a major driver of the introduction and spread of SARS-CoV-2. Aim: To investigate SARS-CoV-2 genetic diversity in the region of a major transport hub in Germany, we characterized the viral sequence diversity of the SARS-CoV-2 variants circulating in Frankfurt am Main, the city with the largest airport in Germany, from the end of October to the end of December 2020. Methods: In total, we recovered 136 SARS-CoV-2 genomes from nasopharyngeal swab samples. We isolated 104 isolates that were grown in cell culture and RNA from the recovered viruses and subjected them to full-genome sequence analysis. In addition, 32 nasopharyngeal swab samples were directly sequenced. Results and conclusion: We found 28 different lineages of SARS-CoV-2 circulating during the study period, including the variant of concern B.1.1.7 (Δ69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion Δ69/Δ70 in 15% of all sequences, a four base pair (bp) deletion (in 2.9% of sequences) and a single bp deletion (in 0.7% of sequences) in ORF3a, leading to ORF3a truncations. In four sequences (2.9%), an amino acid deletion at position 210 in S was identified. In a single sample (0.7%), both a 9 bp deletion in ORF1ab and a 7 bp deletion in ORF7a were identified. One sequence in lineage B.1.1.70 had an N501Y substitution while lacking the Δ69/70 in S. The high diversity of sequences observed over two months in Frankfurt am Main highlights the persisting need for continuous SARS-CoV-2 surveillance using full-genome sequencing, particularly in cities with international airport connections.

scholarly journals Molecular Genetic Analysis of Cucumber mosaic virus Populations Infecting Pepper Suggests Unique Patterns of Evolution in Korea

2014 ◽  
Vol 104 (9) ◽  
pp. 993-1000 ◽  
Author(s):  
Mi-Kyeong Kim ◽  
Jang-Kyun Seo ◽  
Hae-Ryun Kwak ◽  
Jeong-Soo Kim ◽  
Kook-Hyung Kim ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Molecular Genetic ◽  
Purifying Selection ◽  
Molecular Genetic Analysis ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
Evolutionary Mechanisms

Studying genetic structure and diversity of viruses is important to understand the evolutionary mechanisms that generate and maintain variations in viral populations. Cucumber mosaic virus (CMV) is endemic in most pepper fields in Korea. Currently, no effective methods for control of CMV are available due to many environmental and biological factors such as the extensive evolutionary capacity of CMV. Thus, analyzing the genetic structure of CMV populations may facilitate the development of strategies for the control of CMV. In this study, 252 pepper (Capsicum annuum) samples showing virus symptoms were collected by field surveys performed throughout Korea in 2007. Reverse-transcription polymerase chain reaction analyses revealed that, in total, 165 collected samples were infected with CMV. Forty-five CMV isolates were randomly selected within each regional subpopulation and analyzed by full-genome sequencing. Analyses of genetic diversity showed that the 2b gene of CMV is under weaker purifying selection than the other genes. Based on the phylogenetic analysis of RNA1, the CMV isolates from pepper were divided into three clusters in subgroup I. Our full-genome sequence-based molecular analyses of the CMV Korean population suggest that the subpopulations of CMV have been geographically localized in pepper fields in Korea.

scholarly journals Identification and genetic characterization of equine infectious anemia virus in Western Balkans

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Diana Lupulovic ◽  
Sara Savić ◽  
Delphine Gaudaire ◽  
Nicolas Berthet ◽  
Živoslav Grgić ◽  
...  
Keyword(s):  
Equine Infectious Anemia Virus ◽  
Clinical Signs ◽  
Full Genome Sequence ◽  
Enzyme Linked Immunosorbent Assay ◽  
Full Genome ◽  
Western Balkans ◽  
Full Genome Sequencing ◽  
Horse Population ◽  
Equine Infectious Anemia ◽  
Anemia Virus

Abstract Background Equine infectious anemia (EIA) is a viral disease, caused by the Equine Infectious Anemia virus (EIAV) belonging to the Retroviridae family, genus Lentivirus. Horses (or equids) infected with EIAV are lifelong carriers and they remain contagious for other horses even in the absence of clinical signs. So far, EIAV infection has been reported among horses in North and South America, France, Germany, Italy, Hungary and Romania, with no publication regarding the presence of EIAV in horses in Serbia. To determine the circulation of EIAV among, approximately, the 5000 horses of the Vojvodina region, northern part of Serbia, 316 serum undergone serological testing for EIA. Then, identification and full genome sequencing using next generation sequencing was performed from one EIA positive horse. Results the 316 sera were tested with 3 different commercial agar gel immunodiffusion (AGID) tests and two different commercial enzyme-linked immunosorbent assay (ELISA). With the three AGID kits, 311 (98.4%) among the 316 tested sera were negative and only five (1.6%) sera were positive for EIA. Some discrepancies were seen for the two ELISA kits tested since one exhibited the same results as AGID test and the second gave 295 sera with negative results, five with a positive result and 16 with doubtful outcome. Phylogenetic analysis performed using the full genome sequence showed that EIAV characterized from a horse in Serbia is different from those identify so fare around the world and form a distinct and separate group together with another EIAV strain. Conclusions This study demonstrate for the first time that EIAV is circulating at a low level in the horse population from the Northern part of Serbia. Interestingly, phylogenetic data indicates that this EIAV from the western Balkan region of Europe belongs to a new cluster.

scholarly journals ‘Seq & Destroy’: the full genome sequencing of archived wild type and vaccine rinderpest virus isolates prior to their destruction

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Simon King ◽  
Paulina Rajko-Nenow ◽  
Honorata Ropiak ◽  
Paolo Ribeca ◽  
Carrie Batten ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Sequence Data ◽  
Illumina Miseq ◽  
Start Codon ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Rinderpest Virus ◽  
Full Genome Sequencing ◽  
Historical Epidemiology ◽  
In The Wild

Rinderpest, a once much feared livestock disease, was declared eradicated in 2011, however virus-containing material is still held in laboratories worldwide. Prior to the destruction of our institute’s stocks, we determined the full genome sequence of the distinct samples of rinderpest virus (RPV) in our repository. This data would decipher the historical epidemiology of RPV and allow for recovery of the virus should the need arise. For each sample (n=123), sequencing libraries were prepared using either transposon-based fragmentation of cDNA (Nextera XT DNA Library Prep kit) or single primer isothermal amplification (Trio RNA-Seq kit) and sequenced on the Illumina MiSeq. Regions of low or no coverage were re-sequenced using a Sanger sequencing approach. Examination of the sequences of RPV isolates has shown that the African isolates form a single disparate clade, rather than two separate clades as was previously believed. We have also identified two groups of goat-passaged viruses which have acquired an extra 6 bases in the long untranslated region between the matrix and fusion protein coding sequences, and a group of African isolates where translation of the fusion protein begins from a non-standard start codon (AUA). In addition, the viruses that were force-passaged through alternate hosts such as rabbits or goats, appear to diverge from the clades that represent viruses which were maintained in the wild. Our unique set of sequence data will be invaluable for forensic epidemiology investigations in the event of an unforeseen outbreak and aid in the understanding of the evolution of related morbilliviruses.

scholarly journals Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory

2017 ◽  
Vol 5 (43) ◽  
Author(s):  
Kevin Egan ◽  
Philip Kelleher ◽  
Des Field ◽  
Mary C. Rea ◽  
R. Paul Ross ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Genome Sequence ◽  
In Silico ◽  
Thermophilic Bacterium ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Geobacillus Stearothermophilus ◽  
Biosynthetic Genes ◽  
Content Type

ABSTRACT This paper reports the full genome sequence of the antimicrobial-producing bacterium Geobacillus stearothermophilus DSM 458, isolated in a sugar beet factory in Austria. In silico analysis reveals the presence of a number of novel bacteriocin biosynthetic genes.

Full-genome sequence of a novel myovirus, GF-2, infecting Edwardsiella tarda: comparison with other Edwardsiella myoviral genomes

2015 ◽  
Vol 160 (8) ◽  
pp. 2129-2133 ◽  
Author(s):  
Motoshige Yasuike ◽  
Issei Nishiki ◽  
Yuki Iwasaki ◽  
Yoji Nakamura ◽  
Atushi Fujiwara ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Edwardsiella Tarda ◽  
Full Genome Sequence ◽  
Full Genome

474 Hepatitis B virus genomic markers for hepatocellular carcinoma on full-genome sequencing of 332 patients

2006 ◽  
Vol 44 ◽  
pp. S176-S177
Author(s):  
J.J.Y. Sung ◽  
S.K.W. Tsui ◽  
C.H. Tse ◽  
E.Y.T. Ng ◽  
K.S. Leung ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Genome Sequencing ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
B Virus ◽  
Genomic Markers

scholarly journals Complete Genome Sequence of Bacillus subtilis subsp. subtilis Strain ∆6

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Daniel R. Reuß ◽  
Andrea Thürmer ◽  
Rolf Daniel ◽  
Wim J. Quax ◽  
Jörg Stülke
Keyword(s):  
Bacillus Subtilis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Full Genome Sequence ◽  
Subtilis Strain ◽  
Full Genome ◽  
Biotechnological Applications ◽  
A Genome ◽  
Subtilis Subsp

Bacillus subtilis ∆6 is a genome-reduced strain that was cured from six prophages and AT-rich islands. This strain is of great interest for biotechnological applications. Here, we announce the full-genome sequence of this strain. Interestingly, the conjugative element ICE Bs 1 has most likely undergone self-excision in B. subtilis ∆6.

scholarly journals Complete Genome Sequence of a Human Norovirus Strain from the United States Classified as Genotype GII.P6_GII.6

2018 ◽  
Vol 6 (22) ◽  
Author(s):  
Haifeng Chen ◽  
Shiliang Wang ◽  
Weimin Wang
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
The United States ◽  
Virus Genome ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Virus Genotype

ABSTRACT We report here the complete genome sequence of a GII.6 norovirus strain detected in a clinical fecal specimen from the United States. The virus genome has a length of 7,547 bp and a GC content of 50.1%. Complete norovirus genotyping of the full-genome sequence identified the virus genotype as GII.P6_GII.6.

Sign in / Sign up

Export Citation Format

Share Document