Whole-Genome Analysis of Coxsackievirus B3 Reflects Its Genetic Diversity in China and Worldwide

Abstract Background Coxsackievirus B3 (CVB3) has emerged as an active pathogen in myocarditis, aseptic meningitis, hand, foot, and mouth disease (HFMD), and pancreatitis, and is a heavy burden on public health. However, CVB3 has not been systematically analyzed with regard to whole-genome diversity and recombination. Therefore, this study was undertaken to systematically examine the genetic characteristics of CVB3 based on its whole genome. Methods We combined CVB3 isolates from our national HFMD surveillance and global sequences retrieved from GenBank. Phylogenetic analysis was performed to examine the whole genome variety and recombination forms of CVB3 in China and worldwide. Results Phylogenetic analysis showed that CVB3 strains isolated worldwide could be classified into groups A–E based on the sequence of the entire VP1 region. The predominant CVB3 strains in China belonged to group D, whereas group E CVB3 might be circulated globally compared to other groups. The average nucleotide substitution rate in the P1 region of CVB3 was 4.82 × 10−3 substitutions/site/year. Myocarditis was more common with group A. Groups C and D presented more cases of acute flaccid paralysis, and group D may be more likely to cause HFMD. Multiple recombination events were detected among CVB3 variants, and there were twenty-three recombinant lineages of CVB3 circulating worldwide. Conclusions Overall, this study provides full-length genomic sequences of CVB3 isolates with a wide geographic distribution over a long-term time scale in China, which will be helpful for understanding the evolution of this pathogen. Simultaneously, continuous surveillance of CVB3 is indispensable to determine its genetic diversity in China as well as worldwide.

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Coxsackievirus B4: a Undervalued Pathogen that Associated with Hand, Foot and Mouth Disease Outbreak

10.21203/rs.3.rs-207417/v1 ◽

2021 ◽

Author(s):

Jinbo Xiao ◽

Jianxing Wang ◽

Yong Zhang ◽

Dapeng Sun ◽

Huanhuan Lu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Evolutionary Dynamics ◽

Foot And Mouth Disease ◽

Population Diversity ◽

Mouth Disease ◽

Nucleotide Substitution Rate ◽

Genetic Characteristics ◽

Coxsackievirus B4 ◽

Foot And Mouth ◽

Major Outbreak

Abstract Objectives: This study was conducted to discover the causes of Coxsackievirus B4 (CVB4) -induced hand, foot, and mouth disease (HFMD) outbreaks and its evolutionary characteristics.Methods: In this study, we sequenced isolates obtained during the outbreak for comparative analyses with previously sequenced strains. Phylogenetic analysis and evolutionary dynamics were performed to illustrate the genetic characteristics of CVB4 in China and worldwide.Results: The nucleotide sequence of CVB4 isolated during the outbreak in 2011 was more similar to that of CVB4 isolated in Shandong Province, China in 2010 (95.7–99.4%) than to other CVB4 isolated in China (90.9–98.8%). A phylogenetic analysis showed that CVB4 originated from a common ancestor in Shandong. CVB4 strains isolated worldwide could be classified into genotypes A–E according to the VP1 region. All CVB4 strains in China belonged to genotype E. The global population diversity of CVB4 fluctuated substantially over time, and CVB4 isolated from China accounted for a significant increase in diversity of CVB4. The average nucleotide substitution rate in VP1 of Chinese CVB4 (5.20 × 10-3 substitutions/site/year) was slightly higher than that of global CVB4 (4.82 × 10-3 substitutions/site/year). Conclusions: These findings explain both the 2011 outbreak and a global increase in CVB4 diversity. In addition to improving our understanding of a major outbreak, these findings provide a basis for the development of surveillance strategies.

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Genetic characterization of skull base chondrosarcomas

Journal of Neurosurgery ◽

10.3171/2014.12.jns142059 ◽

2015 ◽

Vol 123 (4) ◽

pp. 1036-1041 ◽

Cited By ~ 9

Author(s):

Hiroki Kanamori ◽

Yohei Kitamura ◽

Tokuhiro Kimura ◽

Kazunari Yoshida ◽

Hikaru Sasaki

Keyword(s):

Skull Base ◽

Case Series ◽

Bone Neoplasms ◽

Comparative Genomic ◽

Whole Genome ◽

Whole Genome Analysis ◽

Genetic Characteristics ◽

Genome Study ◽

Skull Base Chordomas

OBJECT Although chondrosarcomas rarely arise in the skull base, chondrosarcomas and chordomas are the 2 major malignant bone neoplasms occurring at this location. The distinction of these 2 tumors is important, but this distinction is occasionally problematic because of radiological and histological overlap. Unlike chordoma and extracranial chondrosarcoma, no case series presenting a whole-genome analysis of skull base chondrosarcomas (SBCSs) has been reported. The goal of this study is to clarify the genetic characteristics of SBCSs and contrast them with those of chordomas. METHODS The authors analyzed 7 SBCS specimens for chromosomal copy number alterations (CNAs) using comparative genomic hybridization (CGH). They also examined IDH1 and IDH2 mutations and brachyury expression. RESULTS In CGH analyses, the authors detected CNAs in 6 of the 7 cases, including chromosomal gains of 8q21.1, 19, 2q22-q32, 5qcen-q14, 8q21-q22, and 15qcen-q14. Mutation of IDH1 was found with a high frequency (5 of 7 cases, 71.4%), of which R132S was most frequently mutated. No IDH2 mutations were found, and immunohistochemical staining for brachyury was negative in all cases. CONCLUSIONS To the best of the authors' knowledge, this is the first whole-genome study of an SBSC case series. Their findings suggest that these tumors are molecularly consistent with a subset of conventional central chondrosarcomas and different from skull base chordomas.

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Molecular Epidemiology of Rabies in Wild Canidae in Tunisia

Viruses ◽

10.3390/v13122473 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2473

Author(s):

Zied Bouslama ◽

Habib Kharmachi ◽

Nourhene Basdouri ◽

Jihen Ben Salem ◽

Samia Ben Maiez ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Wild Animals ◽

Genetic Characteristics ◽

Bayesian Phylogenetic Analysis ◽

Viral Sequencing ◽

Virus Isolates ◽

Virus Strains ◽

Natural Barrier

Rabies is a viral zoonosis that is transmissible to humans via domestic and wild animals. There are two epidemiological cycles for rabies, the urban and the sylvatic cycles. In an attempt to study the epidemiological role of wild canidae in rabies transmission, the present study aimed to analyze the genetic characteristics of virus isolates and confirm prior suggestions that rabies is maintained through a dog reservoir in Tunisia. Virus strains isolated from wild canidae were subject to viral sequencing, and Bayesian phylogenetic analysis was performed using Beast2 software. Essentially, the virus strains isolated from wild canidae belonged to the Africa-1 clade, which clearly diverges from fox-related strains. Our study also demonstrated that genetic characteristics of the virus isolates were not as distinct as could be expected if a wild reservoir had already existed. On the contrary, the geographic landscape is responsible for the genetic diversity of the virus. The landscape itself could have also acted as a natural barrier to the spread of the virus.

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Whole-Genome Analysis of Porcine Circovirus Type 2 in Russia

Pathogens ◽

10.3390/pathogens10121631 ◽

2021 ◽

Vol 10 (12) ◽

pp. 1631

Author(s):

Sergei Raev ◽

Anton Yuzhakov ◽

Taras Aliper

Keyword(s):

Genetic Diversity ◽

Genome Analysis ◽

Porcine Circovirus Type ◽

Porcine Circovirus Type 2 ◽

Porcine Circovirus ◽

Economic Losses ◽

Whole Genome ◽

Whole Genome Analysis ◽

Reading Frame

Porcine circovirus type 2 (PCV2) is the causative agent of porcine circovirus-associated diseases (PCVAD) that bring about significant economic losses in the pig industry all over the world. The aim of this study was to investigate the genetic diversity of PCV2 in Russia and characterize the available complete genome sequences. PCV2 DNA was detected at all investigated farms located in different regions of Russia. Whole-genome analysis demonstrated that the majority of PCV2 strains belonged to genotype PCV2d (12 out of 14), while PCV2a and PCV2b were only detected at 2 farms (one at each). Further analysis revealed that all antibody recognition sites in Russian PCV2 strains were different from the corresponding epitopes in a PCV2a vaccine strain, suggesting that PCV2a-based vaccines may only provide limited protection against these strains. PCV2d strains could be grouped into 3 distinct lines which shared 98.7–100% identity within open reading frame 2 (ORF2). It is the first study reporting the genetic diversity of PCV2 strains in Russia. Our data indicated that, similarly to China, Europe, and USA, PCV2a and PCV2b have largely been replaced by PCV2d.

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Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination

Infection Genetics and Evolution ◽

10.1016/j.meegid.2017.02.008 ◽

2017 ◽

Vol 50 ◽

pp. 38-48 ◽

Cited By ~ 18

Author(s):

Mika Ito ◽

Moegi Kuroda ◽

Tsuneyuki Masuda ◽

Masataka Akagami ◽

Kei Haga ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Analysis ◽

Whole Genome ◽

Whole Genome Analysis

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Phylogenetic and whole genome analysis of first seven SARS-CoV-2 isolates in Bangladesh

Future Virology ◽

10.2217/fvl-2020-0201 ◽

2020 ◽

Vol 15 (11) ◽

pp. 735-746

Author(s):

Nadim Sharif ◽

Shuvra K Dey

Keyword(s):

Phylogenetic Analysis ◽

Saudi Arabia ◽

Genome Analysis ◽

Untranslated Region ◽

Sequence Similarity ◽

Effective Vaccine ◽

Whole Genome ◽

Neighbor Joining ◽

Whole Genome Analysis ◽

Respiratory Coronavirus

Aim: Whole genome and peptide mutation analysis can specify effective vaccine and therapeutics against severe acute respiratory coronavirus-2 (SARS-CoV-2). Materials & methods: Whole genome similarity for Bangladeshi SARS-CoV-2 was determined using ClustalW and BLASTn. Phylogenetic analysis was conducted using neighbor-joining method. Results: 100% of isolates in Bangladesh were in the G clade. We found 99.98–100% sequence similarity among Bangladeshi isolates and isolates of England, Greece, USA, Saudi Arabia and India. Deletion of bases at 5′ untranslated region and 3′ untranslated region was detected. Substitution 261 (E→D) at NSP13 and 1109 (F→L) at spike (S) protein were detected. Substitution 377 (D→G) at nucleocapsid with common substitution 614 (D→G) at S were also detected. Conclusion: This study will provide baseline data for development of an effective vaccine or therapeutics against SARS-CoV-2.

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Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

Viruses ◽

10.3390/v12111262 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1262

Author(s):

Joshua O. Amimo ◽

Eunice M. Machuka ◽

Edward O. Abworo ◽

Anastasia N. Vlasova ◽

Roger Pelle

Keyword(s):

Genetic Diversity ◽

Nucleotide Sequence ◽

Epitope Prediction ◽

Whole Genome Sequence ◽

Diagnostic Tools ◽

Whole Genome ◽

Potential Candidate ◽

Whole Genome Analysis ◽

Porcine Astrovirus ◽

Sequence Identities

Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.

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Genetic Diversity of the Ordinary Strain of Potato virus Y (PVY) and Origin of Recombinant PVY Strains

Phytopathology ◽

10.1094/phyto-10-10-0284 ◽

2011 ◽

Vol 101 (7) ◽

pp. 778-785 ◽

Cited By ~ 73

Author(s):

Alexander V. Karasev ◽

Xiaojun Hu ◽

Celeste J. Brown ◽

Camille Kerlan ◽

Olga V. Nikolaeva ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Tree ◽

Potato Virus ◽

Potato Virus Y ◽

Molecular Study ◽

The United States ◽

Whole Genome ◽

Whole Genome Analysis ◽

Severe Stunting ◽

Ordinary Strain

The ordinary strain of Potato virus Y (PVY), PVYO, causes mild mosaic in tobacco and induces necrosis and severe stunting in potato cultivars carrying the Ny gene. A novel substrain of PVYO was recently reported, PVYO-O5, which is spreading in the United States and is distinguished from other PVYO isolates serologically (i.e., reacting to the otherwise PVYN-specific monoclonal antibody 1F5). To characterize this new PVYO-O5 subgroup and address possible reasons for its continued spread, we conducted a molecular study of PVYO and PVYO-O5 isolates from a North American collection of PVY through whole-genome sequencing and phylogenetic analysis. In all, 44 PVYO isolates were sequenced, including 31 from the previously defined PVYO-O5 group, and subjected to whole-genome analysis. PVYO-O5 isolates formed a separate lineage within the PVYO genome cluster in the whole-genome phylogenetic tree and represented a novel evolutionary lineage of PVY from potato. On the other hand, the PVYO sequences separated into at least two distinct lineages on the whole-genome phylogenetic tree. To shed light on the origin of the three most common PVY recombinants, a more detailed phylogenetic analysis of a sequence fragment, nucleotides 2,406 to 5,821, that is present in all recombinant and nonrecombinant PVYO genomes was conducted. The analysis revealed that PVYN:O and PVYN-Wi recombinants acquired their PVYO segments from two separate PVYO lineages, whereas the PVYNTN recombinant acquired its PVYO segment from the same lineage as PVYN:O. These data suggest that PVYN:O and PVYN-Wi recombinants originated from two separate recombination events involving two different PVYO parental genomes, whereas the PVYNTN recombinants likely originated from the PVYN:O genome via additional recombination events.

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Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic

10.1101/2021.02.09.21251402 ◽

2021 ◽

Author(s):

P.W.G. Mallon ◽

F. Crispie ◽

G. Gonzalez ◽

W. Tinago ◽

A.A. Garcia Leon ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Whole Genome Sequencing ◽

Disease Severity ◽

Genome Sequencing ◽

Population Level ◽

Whole Genome ◽

Multiple Introductions ◽

Relative Contribution ◽

The Impact

AbstractBackgroundWhole-genome sequencing (WGS) of SARS-CoV-2 laboratory-confirmed cases can provide insights into viral transmission and genetic diversity at a population level. However, less is known about the impact of non-pharmaceutical interventions (NPIs), including ‘lockdowns’, on circulating SARS-CoV-2 lineages and variants of concern, the relative contribution of travel to re-emergence of pandemic waves within communities or how different lineages and variants contribute to disease severity.MethodsWe have conducted an analysis within a prospective, multicentre observational study of individuals attending four hospitals in the South-East of Ireland with COVID-19. Samples underwent WGS from which lineages and variants were assigned, lineage frequency was plotted over time and phylogenetic analysis was employed to determine the origin of variants detected post-lockdown. Univariate and multivariate analyses assessed relationships between viral lineage/variant and COVID-19 disease severity.ResultsWe analysed 225 genome sequences across two SARS-CoV-2 waves, 134 (59.6%) from wave 1 (March to June) and 91 (40.4%) from wave 2 (July to December), representing 15.2% of COVID-19 admissions to these hospitals during the sampling periods. Four variants (B.1.1.162, B1.1.70, B.1.1.267 and B.1.1) comprised 68% of variants detected during wave 1. Of these variants, only a single B.1.1.70 sequence was detected in wave 2, while the B.1.177 lineage emerged and contributed to 82.3% of lineages detected. Phylogenetic analysis suggested multiple introductions of wave 2 variants from outside Ireland. We found no consistent association between SARS-CoV-2 lineages and disease severity.ConclusionsThese data suggest elimination of common SARS-CoV-2 lineages from hospitalised cases associated with effective NPIs and that importation of new viral variants through travel was a significant contributor to the re-emergence of the pandemic in the second wave in Ireland. Our findings highlight the importance of genomic surveillance in identifying circulating viral genetic diversity and variants of concern and, also, modelling the disease burden of SARS-CoV-2.

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Evaluation of probiotic characteristics and whole genome analysis of Pediococcus pentosaceus MR001 for use as probiotic bacteria in shrimp aquaculture

Scientific Reports ◽

10.1038/s41598-021-96780-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Warapond Wanna ◽

Komwit Surachat ◽

Panmile Kaitimonchai ◽

Amornrat Phongdara

Keyword(s):

Digestive Enzyme ◽

Shrimp Aquaculture ◽

Control Group ◽

Immune Gene ◽

Whole Genome ◽

Feeding Trial ◽

Intestinal Histology ◽

Whole Genome Analysis ◽

Genetic Characteristics ◽

Pediococcus Pentosaceus

AbstractThe development of non-antibiotic and environmentally friendly agents is a key consideration for health management in shrimp aquaculture. In this study, the probiotic potential in shrimp aquaculture of Pediococcus pentosaceus MR001, isolated from Macrobrachium rosenbergii, was investigated by means of feeding trial and genetic characterization. In the feeding trial, dietary supplementation with P. pentosaceus MR001 significantly increased weight gain and digestive enzyme activity (p < 0.05) in shrimp, Litopenaeus vannamei. The intestinal histology showed that shrimp given the probiotic diet had healthier guts than the control group. Also, the immune gene expression and the survival rate in the treatment group were significantly increased when compared with the control group. The genetic characteristics of P. pentosaceus strain MR001 were explored by performing whole-genome sequencing (WGS) using the HiSeq 2500 platform and PacBio system, revealing the complete circular genome of 1,804,896 bp. We also identified 1789 coding genes and subsequently characterized genes related to the biosynthesis of bacteriocins, stress resistance, and bile tolerance. Our findings suggest that insights in the functional and genetic characteristics of P. pentosaceus strain MR001 could provide opportunities for applications of such strain in shrimp diet supplementation.

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