Genotypes and phylogenetic analysis of adenovirus in children with respiratory infection in Buenos Aires, Argentina (2000–2018)

Human adenoviruses (HAdV) are one of the most frequent causes of respiratory infections around the world, causing mild to severe disease. In Argentina, many studies focused on the association of HAdV respiratory infection with severe disease and fatal outcomes leading to the discovery in 1984 of a genomic variant 7h associated with high fatality. Although several molecular studies reported the presence of at least 4 HAdV species (B, C, D and E) in Argentina, few sequences were available in the databases. In this study, sequences from the hexon gene region were obtained from 141 patients as a first approach to assess the genetic diversity of HAdVs circulating in Buenos Aires, Argentina. Phylogenetic analysis of these sequences and others recovered from public databases confirmed the circulation of the four above-mentioned species represented by 11 genotypes, with predominance in species B and C and shifts in their proportion in the studied period (2000 to 2018). The variants detected in Argentina, for most of the genotypes, were similar to those already described in other countries. However, uncommon lineages belonging to genotypes C2, C5 and E4 were detected, which might indicate the circulation of local variants and will deserve further studies of whole-genome sequences.

Download Full-text

The emergence of SARS-CoV-2 by an unusual genome reconstitution

10.21203/rs.3.rs-33201/v1 ◽

2020 ◽

Author(s):

Seong-Tshool Hong ◽

Md. Mehedi Hassan ◽

Shirina Sharmin ◽

Jinny Hong ◽

Hoi-Seon Lee ◽

...

Keyword(s):

Amino Acids ◽

Phylogenetic Analysis ◽

Pairwise Comparison ◽

Surface Protein ◽

Plasmodium Malariae ◽

Spike Protein ◽

Genome Sequences ◽

The World ◽

The Common ◽

Virus Strains

Abstract SARS-CoV-2 has been spreading remarkedly fast around the world since its emergence while the origin of the virus remains ambiguous. Here, we constructed all of the original prototype genome sequences of SARS-CoV-2 by selecting the common nucleotide among the different virus strains with species. Phylogenetic analysis on the prototype sequences showed that SARS-CoV-2 was a direct descendant of Bat-CoV and was closely related to Pan-CoV, Bat-SL-CoV, and SARS-CoV. The pairwise comparison of SARS-CoV-2 with Bat-CoV showed an unusual replacement of the motif consisting of 7 amino acids within the spike protein of SARS-CoV-2. Database searches showed that the motif originated from a surface protein of Plasmodium malariae, suggesting that the SARS-CoV-2 was emerged after acquiring the motif of the malaria surface protein.

Download Full-text

Analyzing hCov genome sequences: Applying Machine Intelligence and beyond

10.1101/2020.06.03.131987 ◽

2020 ◽

Author(s):

Shashata Sawmya ◽

Arpita Saha ◽

Sadia Tasnim ◽

Naser Anjum ◽

Md. Toufikuzzaman ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Deep Learning ◽

Evolutionary History ◽

Genetic Material ◽

Machine Intelligence ◽

Genome Sequences ◽

Analysis Pipeline ◽

Learning Techniques ◽

The World ◽

Novel Virus

AbstractCovid-19 pandemic, caused by the sars-cov-2 strain of coronavirus, has affected millions of people all over the world and taken thousands of lives. It is of utmost importance that the character of this deadly virus be studied and its nature be analysed. We present here an analysis pipeline comprising phylogenetic analysis on strains of this novel virus to track its evolutionary history among the countries uncovering several interesting relationships, followed by a classification exercise to identify the virulence of the strains and extraction of important features from its genetic material that are used subsequently to predict mutation at those interesting sites using deep learning techniques. In a nutshell, we have prepared an analysis pipeline for hCov genome sequences leveraging the power of machine intelligence and uncovered what remained apparently shrouded by raw data.

Download Full-text

Enterovirus D68 in Viet Nam (2009-2015)

Wellcome Open Research ◽

10.12688/wellcomeopenres.11558.1 ◽

2017 ◽

Vol 2 ◽

pp. 41 ◽

Cited By ~ 6

Author(s):

Nguyen Thi Han Ny ◽

Nguyen To Anh ◽

Vu Thi Ty Hang ◽

Lam Anh Nguyet ◽

Tran Tan Thanh ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Respiratory Infection ◽

Evolutionary Rate ◽

Respiratory Infections ◽

Phylogenetic Reconstruction ◽

Viet Nam ◽

Specific Pcr ◽

Referral Hospitals ◽

The Usa ◽

Enterovirus D68

Background: Since 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015. Methods: Enterovirus/rhinovirus PCR positive respiratory or CSF samples taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included samples were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam 2009-2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively. Results: EV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory samples but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 – 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E-3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008. Conclusions: We have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.

Download Full-text

Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

10.1101/2020.04.14.041301 ◽

2020 ◽

Cited By ~ 3

Author(s):

Aditi Joshi ◽

Sushmita Paul

Keyword(s):

Phylogenetic Analysis ◽

Positive Selection ◽

Whole Genome Sequence ◽

Special Focus ◽

The Novel ◽

Genome Sequences ◽

Travel History ◽

The World ◽

Viral Sequences ◽

Nsp3 Gene

AbstractRecently classified as a pandemic by WHO, novel Corononavirus 2019 has affected almost every corner of the globe causing human deaths in a range of hundred thousands. The virus having its roots in Wuhan (China) has been spread over the world by its own property to change itself accordingly. These changes correspond to its transmission and pathogenicity due to which the concept of social distancing appeared into the picture. In this paper, a few findings from the whole genome sequence analysis of viral genome sequences submitted from India are presented. The data used for analysis comprises 440 collective genome sequences of virus submitted in GenBank, GISAID, and SRA projects, from around the world as well as 28 viral sequences from India. Multiple sequence alignment of all genome sequences was performed and analysed. A novel non-synonymous mutation 4809C>T (S1515F) in NSP3 gene of SARS-CoV2 Indian strains is reported along with other frequent and important changes from around the world: 3037C>T, 14408C>T, and 23403A>G. The novel change was observed in samples collected in the month of March, whereas was found to be absent in samples collected in January with the respective persons’ travel history to China. Phylogenetic analysis clustered the sequences with this change as one separate clade. Mutation was predicted as stabilising change by insilco tool DynaMut. A second patient in the world to our knowledge with multiple (Wuhan and USA) strain contraction was observed in this study. The infected person is among the two early infected patients with travel history to China. Strains sequenced in Iran stood out to have different variants, as most of the reported frequent variants were not observed. The objective of this paper is to highlight the similarities and changes observed in the submitted Indian viral strains. This helps to keep track on the activity, that how virus is changing into a new subtype. Major strains observed were European with the novel change in India and other being emergent clade of Iran. Its important to observe the changes in NSP3 gene, as this gene has been reported with extensive positive selection as well as potential drug target. Extensive Positive Selection Drives the Evolution of Nonstructural Proteins. With the limited number of sequences this was the only frequent novel non-synonymous change observed from Indian strains, thereby making this change vulnerable for investigation in future. This paper has a special focus on tracking of Indian viral sequences submitted in public domain.

Download Full-text

Enterovirus D68 in Viet Nam (2009-2015)

Wellcome Open Research ◽

10.12688/wellcomeopenres.11558.2 ◽

2018 ◽

Vol 2 ◽

pp. 41 ◽

Cited By ~ 1

Author(s):

Nguyen Thi Han Ny ◽

Nguyen To Anh ◽

Vu Thi Ty Hang ◽

Lam Anh Nguyet ◽

Tran Tan Thanh ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Respiratory Infection ◽

Evolutionary Rate ◽

Respiratory Infections ◽

Phylogenetic Reconstruction ◽

Viet Nam ◽

Specific Pcr ◽

Referral Hospitals ◽

The Usa ◽

Enterovirus D68

Background: Since 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015. Methods: Enterovirus/rhinovirus PCR positive respiratory or CSF samples taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included samples were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam 2009 2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively. Results: EV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory samples but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 – 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E -3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008. Conclusions: We have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.

Download Full-text

In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh

10.1101/2020.07.20.212563 ◽

2020 ◽

Author(s):

Tushar Ahmed Shishir ◽

Iftekhar Bin Naser ◽

Shah M. Faruque

Keyword(s):

Phylogenetic Analysis ◽

Protein Structures ◽

Spike Protein ◽

Whole Genome ◽

Missense Mutations ◽

Coding Region ◽

Genome Sequences ◽

Genomic Variations ◽

Southern District ◽

The World

AbstractThe COVID19 pandemic caused by SARS-CoV-2 virus has severely affected most countries of the world including Bangladesh. We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Phylogenetic analysis indicated that the pathogen was imported in Bangladesh from multiple countries. The viruses found in the southern district of Chattogram were closely related to strains from Saudi Arabia whereas those in Dhaka were similar to that of United Kingdom and France. The 64 SARS-CoV-2 sequences from Bangladesh belonged to three clusters. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. Among these, 99 missense mutations (90%) were predicted to destabilize protein structures. Remarkably, a mutation that leads to an I300F change in the nsp2 protein and a mutation leading to D614G change in the spike protein were prevalent in SARS-CoV-2 genomic sequences, and might have influenced the epidemiological properties of the virus in Bangladesh.

Download Full-text

In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh

PLoS ONE ◽

10.1371/journal.pone.0245584 ◽

2021 ◽

Vol 16 (1) ◽

pp. e0245584

Author(s):

Tushar Ahmed Shishir ◽

Iftekhar Bin Naser ◽

Shah M. Faruque

Keyword(s):

Phylogenetic Analysis ◽

Protein Structures ◽

Spike Protein ◽

Whole Genome ◽

Missense Mutations ◽

Coding Region ◽

Genome Sequences ◽

Genomic Variations ◽

Southern District ◽

The World

The COVID19 pandemic caused by SARS-CoV-2 virus has severely affected most countries of the world including Bangladesh. We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Phylogenetic analysis indicated that the pathogen was imported in Bangladesh from multiple countries. The viruses found in the southern district of Chattogram were closely related to strains from Saudi Arabia whereas those in Dhaka were similar to that of United Kingdom and France. The 64 SARS-CoV-2 sequences from Bangladesh belonged to three clusters. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. Among these, 99 missense mutations (90%) were predicted to destabilize protein structures. Remarkably, a mutation that leads to an I300F change in the nsp2 protein and a mutation leading to D614G change in the spike protein were prevalent in SARS-CoV-2 genomic sequences, and might have influenced the epidemiological properties of the virus in Bangladesh.

Download Full-text

Identification of maize mosaic virus by immunoelectron microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100142827 ◽

1986 ◽

Vol 44 ◽

pp. 240-241

Author(s):

O. E. Bradfute

Keyword(s):

Zea Mays ◽

Mosaic Virus ◽

Immunoelectron Microscopy ◽

Severe Disease ◽

Maize Mosaic Virus ◽

The World ◽

Plant Rhabdovirus

Maize mosaic virus (MMV) causes a severe disease of Zea mays in many tropical and subtropical regions of the world, including the southern U.S. (1-3). Fig. 1 shows internal cross striations of helical nucleoprotein and bounding membrane with surface projections typical of many plant rhabdovirus particles including MMV (3). Immunoelectron microscopy (IEM) was investigated as a method for identifying MMV. Antiserum to MMV was supplied by Ramon Lastra (Instituto Venezolano de Investigaciones Cientificas, Caracas, Venezuela).

Download Full-text

From the Tower of London to the Thomas More Society of Buenos Aires: “Give me thy grace, good Lord, to set the world at nought”

Moreana ◽

10.3366/more.2005.42.4.13 ◽

2005 ◽

Vol 42 (Number 164) (4) ◽

pp. 187-206

Author(s):

Clare M. Murphy

Keyword(s):

Buenos Aires ◽

Short History ◽

Thomas More ◽

Tower Of London ◽

Hebrew Poetry ◽

Prayer Book ◽

The World ◽

History Of ◽

Book Of Hours ◽

Almost All

The Thomas More Society of Buenos Aires begins or ends almost all its events by reciting in both English and Spanish a prayer written by More in the margins of his Book of Hours probably while he was a prisoner in the Tower of London. After a short history of what is called Thomas More’s Prayer Book, the author studies the prayer as a poem written in the form of a psalm according to the structure of Hebrew poetry, and looks at the poem’s content as a psalm of lament.

Download Full-text

THE 2019 NOVEL PANDEMIC OF CORONAVIRUS DISEASE (COVID-19): A STUDY OF EXISTING EVIDENCE IN THE INDIAN POPULATION

Era s journal of medical research ◽

10.24041/ejmr2020.33 ◽

2020 ◽

Vol 7 (2) ◽

pp. 199-204

Author(s):

Shrikant Verma ◽

Mohammad Abbas ◽

Sushma Verma ◽

Syed Tasleem Raza ◽

Farzana Mahdi

Keyword(s):

Disease Transmission ◽

Indian Population ◽

Respiratory Infections ◽

Clinical Signs ◽

Case Fatality ◽

Public Health Emergency ◽

The World ◽

And Control ◽

General Wellbeing ◽

Different Parts

A novel spillover coronavirus (nCoV), with its epicenter in Wuhan, China's People's Republic, has emerged as an international public health emergency. This began as an outbreak in December 2019, and till November eighth, 2020, there have been 8.5 million affirmed instances of novel Covid disease2019 (COVID-19) in India, with 1,26,611 deaths, resulting in an overall case fatality rate of 1.48 percent. Coronavirus clinical signs are fundamentally the same as those of other respiratory infections. In different parts of the world, the quantity of research center affirmed cases and related passings are rising consistently. The COVID- 19 is an arising pandemic-responsible viral infection. Coronavirus has influenced huge parts of the total populace, which has prompted a global general wellbeing crisis, setting all health associations on high attentive. This review sums up the overall landmass, virology, pathogenesis, the study of disease transmission, clinical introduction, determination, treatment, and control of COVID-19 with the reference to India.

Download Full-text