Morris S Jones

Morris S Jones
United States Department of Agriculture | USDA · Agricultural Research Service (ARS)

Ph.D.

About

80
Publications
441,981
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
5,378
Citations

Publications

Publications (80)
Article
Full-text available
The family Adenoviridae includes non-enveloped viruses with linear dsDNA genomes of 25–48 kb and medium-sized icosahedral capsids. Adenoviruses have been discovered in vertebrates from fish to humans. The family is divided into six genera, each of which is more common in certain animal groups. The outcome of infection may vary from subclinical to l...
Article
Full-text available
Genomics analysis of a historically-intriguing and predicted emergent human adenovirus (HAdV) pathogen, which caused pneumonia and death, provides insight into a novel molecular evolution pathway involving “ping-pong” zoonosis and anthroponosis. The genome of this promiscuous pathogen is embedded with evidence of unprecedented multiple, multidirect...
Research
Full-text available
Versatile virus hops between three primate species-including humans No other emerging pathogen is known to have jumped so frequently from species to species. A virus that killed a six-year-old boy in 1965 has also infected bonobos and chimpanzees in an unprecedented case of viral 'ping-pong' between species. and their colleagues reconstructed the h...
Article
Full-text available
Human adenoviruses (HAdVs) are uniquely important "model organisms" as they have been used to elucidate fundamental biological processes, are recognized as complex pathogens, and are used as remedies for human health. As pathogens, HAdVs may effect asymptomatic or mild and severe symptomatic disease upon their infection of respiratory, ocular, gast...
Article
Full-text available
The original publication of this article [1] was missing the below author that made contributions to the research and the published article:
Article
Full-text available
Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal...
Data
Net charge distribution of the variable regions. Using the same input data as Fig 1, here we show that there is a great deal of charge variability in all of the variable regions. The V3 loop and V2 epitope region, despite being conserved in terms of length and number of glycosylation sites (Fig 1), both show a great deal of variation in net charge,...
Data
Configurational entropy of the peptide backbone. The estimated entropy was obtained using 1200 frames of simulations at 300K (lines) and 450K (circles) from a total 250 ns trajectory, for both the single peptide (black) and after glycosylation (red). The small inset shows a close-up for higher resolution. (EPS)
Data
The HXB2 reference strain gp120 sequence was used to illustrate the association between glycosylation sites and the 8 Cysteines that form disulfide bonds at the base of the variable loops V1-V4. Of the 23 Cys residues in HXB2, 8 form the base of a variable loop, and 5 of the 8 have an adjacent N linked glycosylation site. In contrast, 0 of the 15 C...
Data
Conservation of N-linked glycosylation sites N156 and N160 across 4633 HIV-1 group M sequences arranged by clade. Green indicates the fraction of sequences that contain both N156 and N160; red indicates that N156 is present; purple indicates that N160 is present, and blue indicates the fraction of sequences that lacks both sites. N160 tends to be a...
Data
Glycan-glycan interactions in the context of gp120 trimer of Env spike. Key glycan contacts in the V1V2 region are provided based on 1 us all-atom MD simulations of the fully glycosylated Env spike. The distances between the center of mass (COM) of glycans are shown. Distances are computed for inter-protomeric contacts (A) between glycans 133–156 (...
Data
Conservation of N-linked proximal glycosylation sites between 72 HIV-2 and non-human primate representative lentiviral sequences from the HIV database. The V2 and V3 C-terminal proximal N-linked glycosylation sites at C196 and C331 are particularly well conserved. (EPS)
Data
Fraction of each residue in the V2 and V2g systems that form beta-strand structures. The two blue-labeled “N” residues are the two glycosylated residues and the two red-labeled “C” residues are the two residues that are disulfide bonded. (EPS)
Article
Full-text available
Viruses within human adenovirus species D (HAdV-D) infect epithelia at essentially every mucosal site. Hypervariable loops 1 and 2 of the hexon capsid protein contain epitopes that together form the epsilon determinant for serum neutralization. We report our analyses comparing HAdV-D15, 29, 56, and the recently identified type 69, each with highly...
Article
Full-text available
Author Summary HAdVs are common pathogens in humans, causing disease mainly in eyes, airways and gastrointestinal tract. Most HAdVs are equipped with twelve protruding fiber proteins that mediate attachment to host cell receptor molecules. Recently, a new human gastroenteritis-associated adenovirus (HAdV-52) was identified and classified as the fir...
Article
Full-text available
Listeria monocytogenes is a gram-positive, foodborne bacterium responsible for disease in humans and animals. Listeriolysin O (LLO) is a required virulence factor for the pathogenic effects of L. monocytogenes. Bioinformatics revealed conserved putative epitopes of LLO that could be used to develop monoclonal antibodies against LLO. Continuous and...
Article
Emergent human and simian adenoviruses (HAdVs) may arise from genome recombination. Computational analysis of SAdV type 35 reveals a genome comprising a chassis with elements mostly from two simian adenoviruses, SAdV-B21 and -B27, and regions of high sequence similarity shared with HAdV-B21 and HAdV-B16. Although recombination direction cannot be d...
Article
Full-text available
Genes within the E3 transcription unit of human adenoviruses modulate host immune responses to infection. A comprehensive genomics and bioinformatics analysis of the E3 transcription unit for 38 viruses within human adenovirus species D (HAdV-D) revealed distinct and surprising patterns of homologous recombination. Homologous recombination was iden...
Article
Full-text available
The recent emergence of highly virulent human adenoviruses (HAdVs) with new tissue tropisms underscores the need to determine their ontogeny. Here we report complete high quality genome sequences and analyses for all the previously unsequenced HAdV serotypes (n = 20) within HAdV species D. Analysis of nucleotide sequence variability for these in co...
Article
Full-text available
Unlabelled: For DNA viruses, genetic recombination, addition, and deletion represent important evolutionary mechanisms. Since these genetic alterations can lead to new, possibly severe pathogens, we applied a systems biology approach to study the pathogenicity of a novel human adenovirus with a naturally occurring deletion of the canonical penton...
Chapter
Adenoviruses are viruses that infect vertebrates and can cause human diseases. A range of symptoms and diseases results when specific cells and tissues are infected by specific human adenoviruses, determined in large part by the fiber protein that projects from the capsid. The molecular and cell biology of adenovirus infection and interactions with...
Article
Full-text available
The genome of human adenovirus (HAdV) D30 was sequenced in depth. Sequence assembly and analysis revealed two distinct viral sequences with identical hexon genes, which were the same as the one previously reported for HAdV-D30. However, one of the two viruses was found to be a recombinant of HAdV-D29. Exclusive reliance on serum neutralization can...
Article
Full-text available
In November of 2007 a human adenovirus (HAdV) was isolated from a bronchoalveolar lavage (BAL) sample recovered from a biopsy of an AIDS patient who presented with fever, cough, tachycardia, and expiratory wheezes. To better understand the isolated virus, the genome was sequenced and analyzed using bioinformatic and phylogenomic analysis. The resul...
Article
Full-text available
Human adenovirus species D type 19 (HAdV-D19) has been associated with epidemic keratoconjunctivitis (EKC), a highly inflammatory infection of the ocular surface. Confusion exists regarding the origins of HAdV-D19. The prototype virus (HAdV-D19p) does not cause EKC, while a virus identified later with the identical serologic determinant is a signif...
Article
Full-text available
Five genomes of human subspecies B1 adenoviruses isolated from cases of acute respiratory disease have been sequenced and archived for reference. These include representatives of two prevalent genomic variants of HAdV-7, i.e., HAdV-7h and HAdV-7d2. The other three are HAdV-3/16, HAdV-16 strain E26, and HAdV-3+7 strain Takeuchi. All are recombinant...
Article
The genome of human adenovirus (HAdV) D30 was sequenced in depth. Sequence assembly and analysis revealed two distinct viral sequences, each with an identical hexon gene, the same as previously reported for HAdV-D30. However, one of the two viruses was found to be a recombinant of HAdV-D29. Exclusive reliance on serum neutralization can lead to mis...
Article
Full-text available
Sporadically, HAdVs from species HAdV-C are detected in acute respiratory disease outbreaks. To rapidly type these viruses, we designed real-time PCR assays that detect and discriminate between adenovirus types HAdV-C1, -C2, -C5, and -C6. Sixteen clinical isolates from the California Department of Public Health were used to validate the new assays....
Article
Full-text available
As one of the first five human adenoviruses (HAdVs) to be sequenced, type 17 was important as a reference tool for comparative genomics of recently isolated HAdV pathogens in species D. HAdV-D17 was the first species D adenovirus to be sequenced and was deposited in GenBank in 1999. These genome data were not of high quality, and a redetermination...
Article
Full-text available
Human adenovirus C (HAdV-C) species are a common cause of respiratory infections and can occasionally produce severe clinical manifestations. A deeper understanding of the variation and evolution in species HAdV-C is especially important since these viruses, including HAdV-C6, are used as gene delivery vectors for human gene therapy and in other bi...
Data
Full-text available
Percent identities of the nucleotide coding sequences of loop1 (L1) and loop2 (L2) HAdV-D58 coding regions to homologous sequences from other viruses in species HAdV-D. (PDF)
Data
Full-text available
Percent identities of the nucleotide coding sequences of selected E3 HAdV-D58 coding sequences and their homologs. (PDF)
Article
Full-text available
In February of 1996 a human adenovirus (formerly known as Ad-Cor-96-487) was isolated from the stool of an AIDS patient who presented with severe chronic diarrhea. To characterize this apparently novel pathogen of potential public health significance, the complete genome of this adenovirus was sequenced to elucidate its origin. Bioinformatic and ph...
Article
Full-text available
We propose that human adenoviruses (HAdVs) be identified , characterized, and typed on the basis of complete genome sequence analyses rather than serological approaches. This idea has recently percolated through the community of adeno-virologists. As a result, an open-floor discussion took place at the Ninth International Adenovirus Meeting (Dobogó...
Article
Full-text available
We propose that human adenoviruses (HAdVs) be identified, characterized and typed on the basis of complete genome sequence analyses rather than serological approaches....
Article
Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In this review, the genomic conservation and diversity are examined...
Article
Full-text available
Adenoviral infections are typically acute, self-limiting, and not associated with death. However, we present the genomic and bioinformatics analysis of a novel recombinant human adenovirus (HAdV-D56) isolated in France that caused a rare neonatal fatality, and keratoconjunctivitis in three health care workers who cared for the neonate. Whole genome...
Article
The genome of the sole remaining unsequenced member of species A, human adenovirus type 18 (HAdV-A18), has been sequenced and analyzed. Members of species A are implicated as gastrointestinal pathogens and were shown to be tumorigenic in rodents. These whole genome and in silico proteome data are important as references for reexamining and integrat...
Article
Full-text available
Human adenovirus 14 (HAdV-14) is a recognized causative agent of epidemic febrile respiratory illness (FRI). Last reported in Eurasia in 1963, this virus has since been conspicuously absent in broad surveys, and was never isolated in North America despite inclusion of specific tests for this serotype in surveillance methods. In 2006 and 2007, this...
Article
Full-text available
Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evo...
Article
Full-text available
Increased levels of serum antibody titers against human adenovirus 36 (HAdV-D36) are associated with human obesity and experimental obesity in laboratory animals. While HAdV-D36 has been studied as an infectious agent implicated in obesity for over a decade, the complete genome sequence and its analysis have yet to be reported. A detailed analysis...
Article
Full-text available
Metagenomics and a panmicrobial microarray were used to examine eight live-attenuated viral vaccines. Viral nucleic acids in trivalent oral poliovirus (OPV), rubella, measles, yellow fever, varicella-zoster, multivalent measles/mumps/rubella, and two rotavirus live vaccines were partially purified, randomly amplified, and pyrosequenced. Over half a...
Article
Full-text available
Bats are hosts to a variety of viruses capable of zoonotic transmissions. Because of increased contact between bats, humans, and other animal species, the possibility exists for further cross-species transmissions and ensuing disease outbreaks. We describe here full and partial viral genomes identified using metagenomics in the guano of bats from C...
Article
Full-text available
Novel human adenoviruses (HAdVs) arise from genome recombination. Analysis of HAdV type 55 from an outbreak in China shows a hexon recombination between HAdV-B11 and HAdV-B14, resulting in a genome that is 97.4% HAdV-B14. Sporadic appearances as a re-emergent pathogen and misidentification as “HAdV-B11a” are due to this partial hexon.
Article
Full-text available
Every year, thousands of basic military trainees in each service of the U.S. Armed Forces experience acute respiratory disease. The majority of this disease burden results from infection with human adenoviruses. We designed single- and multiplex assays that detect and discriminate adenovirus types B3, E4, B7, B11, B14, and B21. A total of 116 oroph...
Article
Full-text available
In 2007, the Centers for Disease Control and Prevention (CDC) reported that Human adenovirus type 14 (HAdV-14) infected 106 military personnel and was responsible for the death of one U.S. soldier at Lackland Air Force Base in Texas. Identification of the responsible adenovirus, which had not previously been seen in North America and for which rapi...
Article
Full-text available
Chronic gastrointestinal illness of unknown etiology is a significant problem in the United States. Using a real-time LightCycler PCR assay we detected Blastocystis in nine patients from a metropolitan area of Corvallis, Oregon who presented with diarrhea, abdominal pain, fatigue, joint pain, skin rash and psychiatric co-morbidity. Phylogenetic ana...
Article
Full-text available
In 2005, a human adenovirus strain (formerly known as HAdV-D22/H8 but renamed here HAdV-D53) was isolated from an outbreak of epidemic keratoconjunctititis (EKC), a disease that is usually caused by HAdV-D8, -D19, or -D37, not HAdV-D22. To date, a complete change of tropism compared to the prototype has never been observed, although apparent recomb...
Article
Full-text available
Cardioviruses cause enteric infections in mice and rats which when disseminated have been associated with myocarditis, type 1 diabetes, encephalitis, and multiple sclerosis-like symptoms. Cardioviruses have also been detected at lower frequencies in other mammals. The Cardiovirus genus within the Picornaviridae family is currently made up of two vi...
Article
Full-text available
Recombination in human adenoviruses (HAdV) may confer virulence upon an otherwise nonvirulent strain. The genome sequence of species D HAdV type 22 (HAdV-D22) revealed evidence for recombination with HAdV-D19 and HAdV-D37 within the capsid penton base gene. Bootscan analysis demonstrated that recombination sites within the penton base gene frame th...
Article
Full-text available
Chronic gastrointestinal illness of unknown etiology is a significant problem in the United States. Using a real-time LightCycler PCR assay we detected Blastocystis in nine patients from a metropolitan area of Corvallis, Oregon who presented with diarrhea, abdominal pain, fatigue, joint pain, skin rash and psychiatric co-morbidity. Phylogenetic ana...
Article
Full-text available
Blastocystis is a prevalent enteric protozoan that infects a variety of vertebrates. Infection with Blastocystis in humans has been associated with abdominal pain, diarrhea, constipation, fatigue, skin rash, and other symptoms. Researchers using different methods and examining different patient groups have reported asymptomatic infection, acute sym...
Data
Appendix A – Additional charts.
Data
Full-text available
Appendix B – Characteristics of known gastrointestinal pathogens.
Data
List of Blastocystis studies categorized by researcher finding and geographic location.
Article
Full-text available
We developed a real-time LC PCR assay to detect a 152 bp sequence in an uncharacterized region of the Blastocystis genome. The described assay detected 11 of 11 ATCC strains of Blastocystis from subtypes 1, 3, and 4. Three of three stool samples from Oregon and California military personnel that were negative for Blastocystis by an ova and parasite...
Article
Full-text available
The Cardiovirus genus of the family Picornaviridae includes two distinct species, Encephalomyocarditis virus and Theilovirus. We now report the complete nucleotide sequences of three Theiler's murine encephalomyelitis virus (TMEV) strains (TO Yale, TOB15, and Vie 415HTR) and of Vilyuisk human encephalomyelitis virus (VHEV). This information, togeth...
Article
Plasma pools used in the manufacture of blood- and plasma-derived medicinal products are frequently contaminated with parvovirus B19. The presence of the novel human parvovirus PARV4 and a related variant PARV5 in manufacturing plasma pools was recently demonstrated. Another recently identified parvovirus, human bocavirus (HBoV), has been identifie...
Article
Full-text available
Fever of unknown origin (FUO) is a serious problem in the United States. An unidentified agent was cultured from the stool of an infant who presented with FUO. This virus showed growth in HFDK cells and suckling mice. Using DNase sequence-independent single-primer amplification, we identified several nucleotide sequences with a high homology to The...
Article
Full-text available
An unidentified agent was cultured in primary monkey cells at the Los Angeles County Public Health Department from each of five stool specimens submitted from an outbreak of gastroenteritis. Electron microscopy and an adenovirus-specific monoclonal antibody confirmed this agent to be an adenovirus. Since viral titers were too low, complete serotypi...
Article
Full-text available
Clostridium perfringens is one of the etiologic agents of gas gangrene that can occur when a wound is contaminated with soil. Type A C. perfringens can cause foodborne and nonfoodborne gastrointestinal illnesses due to an enterotoxin (CPE) produced by some strains during sporulation. We developed a quantitative real-time PCR assay based on fluoresc...