scholarly journals Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences

2019 ◽  
Author(s):  
Anna L McNaughton ◽  
Peter Revill ◽  
Margaret Littlejohn ◽  
Philippa C Matthews ◽  
M Azim Ansari
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Unified Approach ◽  
Hbv Genotype ◽  
Dna Virus ◽  
Double Stranded Dna ◽  
B Virus ◽  
Reference Sequences ◽  
Genomic Length

ABSTRACTHepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), thus far characterised. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. An alignment of these reference sequences and maximum-likelihood phylogenetic trees of the sequences are provided to simplify classification. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level.

scholarly journals Circular Double-Stranded Forms of TT Virus DNA in the Liver

2000 ◽  
Vol 74 (11) ◽  
pp. 5161-5167 ◽  
Author(s):  
Hiroaki Okamoto ◽  
Masato Ukita ◽  
Tsutomu Nishizawa ◽  
Junichi Kishimoto ◽  
Yuji Hoshi ◽  
...  
Keyword(s):  
Human Beings ◽  
Specific Primer ◽  
Dna Virus ◽  
S1 Nuclease ◽  
Tt Virus ◽  
Double Stranded Dna ◽  
Replicative Intermediates ◽  
Paired Serum ◽  
Genomic Length ◽  
Liver Tissues

ABSTRACT TT virus (TTV) is an unenveloped, circular, and single-stranded DNA virus commonly infecting human beings worldwide. TTV DNAs in paired serum and liver tissues from three viremic individuals were separated by gel electrophoresis and characterized biophysically. TTV DNAs in sera migrated in sizes ranging from 2.0 to 2.5 kb. TTV DNAs in liver tissues, however, migrated at 2.0 to 2.5 kb as well as at 3.5 to 6.1 kb. Both faster- and slower-migrating forms of TTV DNAs in the liver were found to be circular and of the full genomic length of 3.8 kb. TTV DNAs migrating at 2.0 to 2.5 kb, from either serum or liver tissues, were sensitive to S1 nuclease but resistant to restriction endonucleases, and therefore, they were single-stranded. By contrast, TTV DNAs in liver tissues that migrated at 3.5 to 6.1 kb were resistant to S1 nuclease. They migrated at 3.7 to 4.0 kb after digestion with EcoRI, which suggests that they represent circular, double-stranded replicative intermediates of TTV. When TTV DNAs were subjected to strand-specific primer extension and then amplified by PCR with internal primers, those in serum were found to be minus-stranded DNAs while those in liver tissues were found to be a mixture of plus- and minus-stranded DNAs. These results suggest that TTV replicates in the liver via a circular double-stranded DNA.

A case of hepatitis B virus infection in Eritrean Diciotti migrant: phylogenetic analysis and ‘mirror effect’

2019 ◽  
Vol 14 (8) ◽  
pp. 509-514
Author(s):  
Giancarlo Ceccarelli ◽  
Eleonora Cella ◽  
Serena Vita ◽  
Alessia Lai ◽  
Erika Ebranati ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Copy Number ◽  
Mirror Effect ◽  
Hepatitis B Virus Infection ◽  
Migrant Population ◽  
Hbv Genotype ◽  
B Virus ◽  
Epidemiological Approach

A case of hepatitis B virus (HBV) infection in an Eritrean migrant was described to provide an epidemiological approach based on phylogenetic analysis useful in developing countries with lacking information. Migrant, positive for HBsAg and HBeAg, carried HBV at high copy number. A sequence of HBV HBsAg region was used for phylogenetic relationships and genetic variability investigation. In the phylogenetic tree, the sequence corresponded to D2 HBV genotype and the cluster root dated 7 years ago. These data compared with the date of landing in Italy, suggest that he was infected at least 7 years before his arrival. This approach by ‘mirror effect’ allows the reconstruction of HBV epidemiology in the country of origin, analyzing the migrant population in the host country.

scholarly journals Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan

2021 ◽  
Vol 9 (12) ◽  
pp. 2609
Author(s):  
Atia Basheer ◽  
Imran Zahoor
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Reference Genome ◽  
Third Wave ◽  
Genomic Epidemiology ◽  
Wave Data ◽  
The World ◽  
Reference Sequences ◽  
First Time ◽  
Second Wave

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.

scholarly journals Inhibition of a Large Double-Stranded DNA Virus by MxA Protein

2008 ◽  
Vol 83 (5) ◽  
pp. 2310-2320 ◽  
Author(s):  
Christopher L. Netherton ◽  
Jennifer Simpson ◽  
Otto Haller ◽  
Thomas E. Wileman ◽  
Haru-Hisa Takamatsu ◽  
...  
Keyword(s):  
Rna Viruses ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Vero Cells ◽  
Dna Virus ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Late Protein ◽  
B Virus ◽  
Negative Sense

ABSTRACT Increasing evidence points to the importance of the interferon (IFN) response in determining the host range and virulence of African swine fever virus (ASFV). Infection with attenuated strains of ASFV leads to the upregulation of genes controlled by IFN pathways, including myxovirus resistance (Mx) genes that are potent effectors of the antiviral state. Mx gene products are known to inhibit the replication of many negative-sense single-stranded RNA viruses, as well as double-stranded RNA viruses, positive-sense single-stranded RNA viruses, and the reverse-transcribing DNA virus hepatitis B virus. Here, we provide data that extend the known range of viruses inhibited by Mx to include the large double-stranded DNA viruses. Stably transfected Vero cells expressing human MxA protein did not support ASFV plaque formation, and virus replication in these cells was reduced 100-fold compared with that in control cells. In contrast, ASFV replication in cells expressing MxB protein or a mutant MxA protein was similar to that in control Vero cells. There was a drastic reduction in ASFV late protein synthesis in MxA-expressing cells, correlating with the results of previous work on the effect of IFN on viral replication. Strikingly, the inhibition of ASFV replication was linked to the recruitment of MxA protein to perinuclear viral assembly sites, where the protein surrounded the virus factories. Interactions between ASFV and MxA were similar to those seen between MxA and different RNA viruses, suggesting a common inhibitory mechanism.

scholarly journals Molecular Phylogeny of Suid Herpesvirus 1

ISRN Virology ◽  
2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Antônio A. Fonseca ◽  
Érica B. Sales ◽  
Marcos B. Heinemann ◽  
Jenner K. P. Reis
Keyword(s):  
Phylogenetic Trees ◽  
Swine Industry ◽  
Dna Virus ◽  
Genetic Sequencing ◽  
Phylogenetic Studies ◽  
Double Stranded Dna ◽  
The World ◽  
Complete Sequences ◽  
Herpesvirus 1 ◽  
Different Parts

Pseudorabies is a disease that significantly impacts the swine industry. This disease is caused by Suid Herpesvirus 1 (SuHV-1), which is a double-stranded DNA virus that belongs to the Herpesviridae family and the Alphaherpesvirinae subfamily and exhibits a slow rate of genetic evolution. The aim of this study was to use both full and partial sequences of SuHV-1 genes available in GenBank to examine the evolution and divergence of viruses isolated in different parts of the world. Partial and complete sequences of SuHV-1 genes were obtained either from GenBank (i.e., us6, us7, us8, us9, ul14, ul49.5, and ul44) or from genetic sequencing of Brazilian SuHV-1 samples. The results of this study corroborate previous phylogenetic studies of SuHV-1 that demonstrated different evolutionary profiles of isolates from different parts of the globe, with a rapid genetic dispersion of Chinese isolates. All of the phylogenetic trees generated in this study demonstrated a large genetic distance between SuHV-1 isolates from the Western and Eastern regions of the world.

Phylogenetic analysis of the genus Cylicocyclus (Nematoda: Strongylidae) based on nuclear ribosomal sequence data

2013 ◽  
Vol 58 (2) ◽  
Author(s):  
Yanzhen Bu ◽  
Hongxing Niu ◽  
Luping Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Internal Transcribed Spacer ◽  
Species Complex ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Its Sequences ◽  
Data Sets ◽  
Reference Sequences ◽  
Second Internal Transcribed Spacer

AbstractSeven species of Cylicocyclus Ihle, 1922 (Nematoda: Strongylidae) were collected from donkeys from Henan Province, China. Five samples of each species were selected for sequencing. Sixteen different internal transcribed spacer (ITS) sequences representing the seven species of Cylicocyclus were obtained. Sequence differences in the first internal transcribed spacer (ITS-1) among species was lower than that of the second internal transcribed spacer (ITS-2). Phylogenetic analyses were conducted using the combined ITS-1 and ITS-2 data sets from the present study and using reference sequences from the GenBank database. The MP and ML trees were similar in topology. The phylogenetic trees were divided into two clades. Clade I included 8 species of Cylicocyclus; within this group, Cylicocyclus leptostomus (Kotlan, 1920) is nested between different samples of Cylicocyclus ashworthi (LeRoux, 1924), suggesting C. ashworthi may represent a species complex. Clade II included Cylicocyclus elongatus (Looss, 1900) and Cylicocyclus ultrajectinus (Ihle, 1920); however, these two species always clustered with the comparative species (Petrovinema poculatum (Looss, 1900) and Poteriostomum imparidentatum Quiel, 1919), suggesting that C. elongatus and C. ultrajectinus represent members of other genera.

scholarly journals Genotype C of hepatitis B virus can be classified into at least two subgroups

2004 ◽  
Vol 85 (2) ◽  
pp. 283-292 ◽  
Author(s):  
Tran Thien-Tuan Huy ◽  
Hiroshi Ushijima ◽  
Vo Xuan Quang ◽  
Khin Maung Win ◽  
Pairoj Luengrojanakul ◽  
...  
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Far East ◽  
Full Length ◽  
Hbv Genotype ◽  
B Virus ◽  
Protein Amino Acids ◽  
Genotype C

A genomic characterization of hepatitis B virus (HBV) was done for 56 pre-S1/pre-S2 genes and 10 full-length HBV genotype C isolates from five Asian countries. Phylogenetic analysis of the pre-S1/pre-S2 genes revealed two major groups within genotype C: one for isolates from southeast Asia including Vietnam, Myanmar and Thailand (named HBV/C1) and the other for isolates from Far East Asia including Japan, Korea and China (named HBV/C2). This finding was confirmed by phylogenetic analysis based on the full-length sequence of 32 HBV genotype C isolates, including 22 from database entries. Two isolates from Okinawa, the island off the southern end of Japan, formed a different branch. Specific amino acid sequence changes were identified in the large S protein (amino acids 51, 54, 60, 62 and 73) and P protein (amino acids 231, 233, 236, 248, 252 and 304). Our results indicate that genotype C of HBV can be classified into at least two subgroups.

scholarly journals Genomic epidemiology of SARS-CoV-2 divulge B.1, B.1.36, and B.1.1.7 as the most dominant lineages in first, second, and third wave of SARS-CoV-2 infections in Pakistan

2021 ◽  
Author(s):  
Atia Basheer ◽  
Imran Zahoor
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Reference Genome ◽  
Third Wave ◽  
Genomic Epidemiology ◽  
Wave Data ◽  
The World ◽  
Reference Sequences ◽  
First Time ◽  
Second Wave

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with their role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3,804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain & coverage map was created by employing Nextclade. And by using the amino acid subsitutions the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following 7 clades G, GH, GR, GRY, L, O, & S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), & B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%) & B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of 9 lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), & Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.

The Tupí-Guaraní language family

Diachronica ◽  
2021 ◽  
Author(s):  
Fabrício Ferraz Gerardi ◽  
Stanislav Reichert
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Genetic Research ◽  
Likelihood Estimation ◽  
Stochastic Algorithm ◽  
Language Family ◽  
Historical Sources ◽  
Bayesian Phylogenetic Analysis

Abstract Attempts to classify Tupí-Guaraní languages have so far been inconsistent with archaeological evidence and ignored information from historical sources. The case of Tupinambá is most illustrative in this regard. Using both Bayesian phylogenetic analysis and a stochastic algorithm that reconstructs phylogenetic trees by relying on maximum likelihood estimation, we suggest a new internal classification of the Tupí-Guaraní branch. The results of the analyses are in accordance with the most recent genetic research on Tupían populations and challenge previous classifications by suggesting, among others, that Tupinambá should not be considered a ‘Guaraní’ language.

A new record and phylogenetic position of Notiosorex crawfordi (Eulipotyphla, Soricidae) with distribution in Zacatecas, Mexico, using mitochondrial DNA

Mammalia ◽  
2020 ◽  
Vol 84 (4) ◽  
pp. 407-412
Author(s):  
Fernando Álvarez-Córdova ◽  
Rogelio Rosas-Valdez ◽  
Elizabeth A. Martínez-Salazar
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
New Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Position ◽  
Morphological Identification

AbstractA unique record of the desert shrew in Zacatecas, Mexico, is known and has been collected since 1897 in the locality “El Plateado” within the municipality of El Plateado de Joaquin Amaro, Zacatecas. On October 2016, two specimens were collected from the municipality of Susticacán, Zacatecas, Mexico. A morphological identification and phylogenetic analysis based on partial sequences of cytochrome b oxidase of mitochondrial DNA (mtDNA) were implemented. Morphology and the phylogenetic trees that were recovered by using maximum-likelihood (ML) confirmed the identity of these specimens as Notiosorex crawfordi. This is the second record for the species in Zacatecas, Mexico, after 121 years.

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