Genome Sequences of Three Species D Adenoviruses Isolated from AIDS Patients

Alkhalaf, Moustafa Alissa; Qurashi, Yasir Mohammed A. Al; Guiver, Malcolm; Cooper, Robert J.

doi:10.1128/genomea.01267-13

Cited by 6 publications

(3 citation statements)

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“…Human adenoviruses (HAdV) are associated in humans with a broad spectrum of clinical diseases, such as acute respiratory disease (ARD), community-acquired pneumonia (CAP), as well as conjunctivitis, gastrointestinal, opportunistic infections in immune-deficient individuals, and possibly, obesity ( Dingle and Langmuir , 1968 ; Chu and Pavan-Langston, 1979 ; Wood, 1988 ; Dhurandhar et al, 1992 ; Kojaoghlanian et al, 2003 ; Hakim and Tleyjeh, 2008 ). Since the first HAdV isolate was found in 1953 ( Hilleman et al, 1953 ; Rowe et al, 1953 ), more than 80 HAdV genotypes have been identified and classified into seven species (A to G) using the whole-genome sequence as the typing standard 1 ( Jones et al, 2007 ; Ishiko et al, 2008 ; Walsh et al, 2009 , 2010 , 2011 ; Liu et al, 2011 , 2012 ; Matsushima et al, 2011 , 2012 , 2013 ; Robinson et al, 2011 , 2013b ; Seto et al, 2011 ; Dehghan et al, 2012 ; Singh et al, 2012 , 2013 ; Zhou et al, 2012 ; Alissa Alkhalaf et al, 2014 ; Hage et al, 2015 ; Hashimoto et al, 2018 ). HAdV species B are further divided into subspecies B1 (HAdV-B3, -B7, -B16, -B21, and -B50) and B2 (HAdV-B11, -B14, -B34, -B35, and -B55) according to their restriction enzyme digestion patterns ( Wadell et al, 1980 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomic Analysis of Re-emergent Human Adenovirus Type 55 Pathogens Associated With Adult Severe Community-Acquired Pneumonia Reveals Conserved Genomes and Capsid Proteins

et al. 2018

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Human adenovirus type 55 (HAdV-B55) is a recently identified acute respiratory disease (ARD) pathogen in HAdV species B with a recombinant genome between renal HAdV-B11 and respiratory HAdV-B14. Since HAdV-B55 first appeared in China school in 2006, no more ARD cases associated with it had been reported until 2011, when there was an outbreak of adult severe community-acquired pneumonia (CAP) in Beijing, China. Reported here is the bioinformatics analysis of the re-emergent HAdV-B55 responsible for this outbreak. Recombination and protein sequence analysis re-confirmed that this isolate (BJ01) was a recombinant virus with the capsid hexon gene from HAdV-B11. The selection pressures for the three capsid proteins, i.e., hexon, penton base, and fiber genes, were all negative, along with very low non-synonymous (dN) and synonymous (dS) substitutions/site (<0.0007). Phylogenetic analyses of the whole genome and the three major capsid genes of HAdV-B55 revealed the close phylogenetic relationship among all HAdV-B55 strains. Comparative genomic analysis of this re-emergent HAdV-B55 strain (BJ01; 2011) with the first HAdV-B55 strain (QS-DLL; 2006) showed the high genome identity (99.87%), including 10 single-nucleotide non-synonymous substitutions, 11 synonymous substitutions, 3 insertions, and one deletion in non-coding regions. The major non-synonymous substitutions (6 of 10) occurred in the protein pVI in its L3 region, which protein has different functions at various stages of an adenovirus infection, and may be associated with the population distribution of HAdV-B55 infection. No non-synonymous substitutions were found in the three major capsid proteins, which proteins are responsible for type-specific neutralizing antibodies. Comparative genomic analysis of the re-emergent HAdV-B55 strains associated with adult severe CAP revealed conserved genome and capsid proteins, providing the foundation for the development of effective vaccines against this pathogen. This study also facilitates the further investigation of HAdV-B55 epidemiology, molecular evolution, patterns of pathogen emergence and re-emergence, and the predication of genome recombination between adenoviruses.

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Section: Introductionmentioning

confidence: 99%

Comparative Genomic Analysis of Re-emergent Human Adenovirus Type 55 Pathogens Associated With Adult Severe Community-Acquired Pneumonia Reveals Conserved Genomes and Capsid Proteins

et al. 2018

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“… estimated the 1‐year actuarial risk of adenovirus infection in persons infected with HIV to be 28%. Multiple, previously unrecognized HAdV‐Ds were discovered during the global AIDS epidemic, including HAdV‐D43‐51, D58, D59, D62, and D75 . In addition, numerous reports detail previously identified viruses that were found to infect AIDs patients .…”

Section: Viral Persistence Host Immune Suppression and The Evolutiomentioning

confidence: 99%

Genomic foundations of evolution and ocular pathogenesis in human adenovirus species D

et al. 2019

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Human adenovirus commonly causes infections of respiratory, gastrointestinal, genitourinary, and ocular surface mucosae. Although most adenovirus eye infections are mild and self-limited, specific viruses within human adenovirus species D are associated with epidemic keratoconjunctivitis (EKC), a severe and highly contagious ocular surface infection, which can lead to chronic and/or recurrent, visually disabling keratitis. In this review, we discuss the links between adenovirus ontogeny, genomics, immune responses, and corneal pathogenesis, for those viruses that cause EKC.

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“…HAdV recombination continuously happens between strains of the same species ( 6 ). Mutations in hexon, fiber, and penton base proteins result in new strains of the adenovirus ( 7 ). The regions of loop1 and 2, and hypervariable regions 1–7 of hexon gene have shown to be highly susceptible to homologous recombination among HAdV-D ( 8 ).…”

Section: Introductionmentioning

confidence: 99%

Evolution and diversity of human adenoviruses isolated from patients with keratoconjunctivitis

Karami¹,

Jalali²,

Jalilian³

et al. 2022

IJM

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Background and Objectives: Human adenovirus type 8 is a highly contagious eye disease and is considered as the most common epidemic keratoconjunctivitis worldwide. The virus may alter the course of detection as mutations and recombina- tion in surface antigens are associated with binding and pathogenesis in human adenovirus. The recognition of new recom- binant human adenovirus has been based on sequencing of three genes, penton base, hexon and fiber. Materials and Methods:50 suspected samples of ocular keratoconjunctivitis were selected over 6 months. Following DNA extraction from isolates positive for cytopathic effect in each well, the complete sequences of hexon, fiber, and penton re- gions were performed on the genome of human adenovirus isolates using PCR. The sequences of capsid genes, including hexon, fiber, and penton were assessed to observe the evidence of recombination at the molecular level using genetic tools. Results: The results of nucleotide and amino acid sequence of 5/ 50 patients with epidemic keratoconjunctivitis positive for hypervariable region of hexon (132 -449), hypervariable of knob fiber (183 -362) and hypervariable penton (106 -466) isolates showed nucleotide and amino acid identity of 98% and 99.41%, 99% and 100%, 95% and 99.72% with hexon, fiber and penton of human adenovirus 8 subtypes. The results of phylogenetic tree and Simplot of the entire sequences and hy- pervariable regions of isolated hexon, fiber and penton showed all the isolates of human adenovirus from Ahvaz, Iran, were clustered with human adenovirus 8A, B, E, P and J, subtypes isolated strains from different regions of the world. Conclusion: The results of this study revealed that the human adenovirus isolates from patients with epidemic keratocon- junctivitis were closed to human adenovirus 8A, B, E, P and J subtypes. To determine the emergence of new human adeno- virus D8 subtypes strain, analysis of complete genome sequence of human adenovirus was required.

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Genome Sequences of Three Species D Adenoviruses Isolated from AIDS Patients

Cited by 6 publications

References 5 publications

Comparative Genomic Analysis of Re-emergent Human Adenovirus Type 55 Pathogens Associated With Adult Severe Community-Acquired Pneumonia Reveals Conserved Genomes and Capsid Proteins

Comparative Genomic Analysis of Re-emergent Human Adenovirus Type 55 Pathogens Associated With Adult Severe Community-Acquired Pneumonia Reveals Conserved Genomes and Capsid Proteins

Genomic foundations of evolution and ocular pathogenesis in human adenovirus species D

Evolution and diversity of human adenoviruses isolated from patients with keratoconjunctivitis

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