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Guan M, Deliberto TJ, Feng A, Zhang J, Li T, Wang S, Li L, Killian ML, Praena B, Giri E, Deliberto ST, Hang J, Olivier A, Torchetti MK, Tao YJ, Parrish C, Wan XF. Neu5Gc binding loss of subtype H7 influenza A virus facilitates adaptation to gallinaceous poultry following transmission from waterbirds but restricts spillback. bioRxiv 2024:2024.01.02.573990. [PMID: 38260375 PMCID: PMC10802348 DOI: 10.1101/2024.01.02.573990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Migratory waterfowl, gulls, and shorebirds serve as natural reservoirs for influenza A viruses, with potential spillovers to domestic poultry and humans. The intricacies of interspecies adaptation among avian species, particularly from wild birds to domestic poultry, are not fully elucidated. In this study, we investigated the molecular mechanisms underlying avian species barriers in H7 transmission, particularly the factors responsible for the disproportionate distribution of poultry infected with A/Anhui/1/2013 (AH/13)-lineage H7N9 viruses. We hypothesized that the differential expression of N-glycolylneuraminic acid (Neu5Gc) among avian species exerts selective pressure on H7 viruses, shaping their evolution and enabling them to replicate and transmit efficiently among gallinaceous poultry, particularly chickens. Our glycan microarray and biolayer interferometry experiments showed that AH/13-lineage H7N9 viruses exclusively bind to Neu5Ac, in contrast to wild waterbird H7 viruses that bind both Neu5Ac and Neu5Gc. Significantly, reverting the V179 amino acid in AH/13-lineage back to the I179, predominantly found in wild waterbirds, expanded the binding affinity of AH/13-lineage H7 viruses from exclusively Neu5Ac to both Neu5Ac and Neu5Gc. When cultivating H7 viruses in cell lines with varied Neu5Gc levels, we observed that Neu5Gc expression impairs the replication of Neu5Ac-specific H7 viruses and facilitates adaptive mutations. Conversely, Neu5Gc deficiency triggers adaptive changes in H7 viruses capable of binding to both Neu5Ac and Neu5Gc. Additionally, we assessed Neu5Gc expression in the respiratory and gastrointestinal tissues of seven avian species, including chickens, Canada geese, and various dabbling ducks. Neu5Gc was absent in chicken and Canada goose, but its expression varied in the duck species. In summary, our findings reveal the crucial role of Neu5Gc in shaping the host range and interspecies transmission of H7 viruses. This understanding of virus-host interactions is crucial for developing strategies to manage and prevent influenza virus outbreaks in diverse avian populations.
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Affiliation(s)
- Minhui Guan
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Thomas J. Deliberto
- US Department of Agriculture Animal and Plant Health Inspection Service, Fort Collins, Colorado, USA
| | - Aijing Feng
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jieze Zhang
- Department of Bioengineering, Rice University, Houston, TX, 77030 USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Shuaishuai Wang
- Department of Chemistry and Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Lei Li
- Department of Chemistry and Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | - Beatriz Praena
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Emily Giri
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Shelagh T Deliberto
- US Department of Agriculture Animal and Plant Health Inspection Service, Fort Collins, Colorado, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Alicia Olivier
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Colin Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA
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Tang CY, Li T, Haynes TA, McElroy JA, Ritter D, Hammer RD, Sampson C, Webby R, Hang J, Wan XF. Rural populations facilitated early SARS-CoV-2 evolution and transmission in Missouri, USA. Npj Viruses 2023; 1:7. [PMID: 38186942 PMCID: PMC10769004 DOI: 10.1038/s44298-023-00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 01/09/2024]
Abstract
In the United States, rural populations comprise 60 million individuals and suffered from high COVID-19 disease burdens. Despite this, surveillance efforts are biased toward urban centers. Consequently, how rurally circulating SARS-CoV-2 viruses contribute toward emerging variants remains poorly understood. In this study, we aim to investigate the role of rural communities in the evolution and transmission of SARS-CoV-2 during the early pandemic. We collected 544 urban and 435 rural COVID-19-positive respiratory specimens from an overall vaccine-naïve population in Southwest Missouri between July and December 2020. Genomic analyses revealed 53 SARS-CoV-2 Pango lineages in our study samples, with 14 of these lineages identified only in rural samples. Phylodynamic analyses showed that frequent bi-directional diffusions occurred between rural and urban communities in Southwest Missouri, and that four out of seven Missouri rural-origin lineages spread globally. Further analyses revealed that the nucleocapsid protein (N):R203K/G204R paired substitutions, which were detected disproportionately across multiple Pango lineages, were more associated with urban than rural sequences. Positive selection was detected at N:204 among rural samples but was not evident in urban samples, suggesting that viruses may encounter distinct selection pressures in rural versus urban communities. This study demonstrates that rural communities may be a crucial source of SARS-CoV-2 evolution and transmission, highlighting the need to expand surveillance and resources to rural populations for COVID-19 mitigation.
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Affiliation(s)
- Cynthia Y. Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- These authors contributed equally: Cynthia Y. Tang, Tao Li
| | - Tricia A. Haynes
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jane A. McElroy
- Family and Community Medicine, University of Missouriś, Columbia, MO, USA
| | - Detlef Ritter
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | - Richard D. Hammer
- Anatomic Pathology & Clinical Pathology, University of Missouri, Columbia, MO, USA
| | | | - Richard Webby
- Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA
- Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA
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Potter-Birriel JM, Pollio AR, Knott BD, Chunashvili T, Fung CK, Conte MA, Reinbold-Wasson DD, Hang J. Metagenomics analysis reveals presence of the Merida-like virus in Georgia. Front Microbiol 2023; 14:1258810. [PMID: 37901812 PMCID: PMC10602647 DOI: 10.3389/fmicb.2023.1258810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023] Open
Abstract
Arbovirus surveillance is fundamental for the discovery of novel viruses and prevention of febrile vector-borne illnesses. Vector-borne pathogens can rapidly expand and adapt in new geographic and environmental conditions. In this study, metagenomic surveillance was conducted to identify novel viruses in the Country of Georgia. A total of 521 mosquitoes were captured near a military training facility and pooled from species Culex pipiens (Linnaeus) (87%) and Aedes albopictus (Skuse) (13%). We decided to further analyze the Culex pipiens mosquitoes, due to the more extensive number of samples collected. Our approach was to utilize an unbiased total RNA-seq for pathogen discovery in order to explore the mosquito virome. The viral reads from this analysis were mostly aligned to Insect-specific viruses from two main families, the Iflaviridae; a positive-stranded RNA virus and the Rhabdoviridae; a negative- and single-stranded RNA virus. Our pathogen discovery analysis revealed viral reads aligning to the Merida-like virus Turkey (MERDLVT) strain among the Rhabdoviridae. To further validate this result, we conducted a BLAST sequence comparison analysis of our samples with the MERDLVT strain. Our positive samples aligned to the MERDLVT strain with 96-100% sequence identity and 99.7-100% sequence coverage. A bootstrapped maximum-likelihood phylogenetic tree was used to evaluate the evolutionary relationships among these positive pooled specimens with the (MERDLVT) strain. The Georgia samples clustered most closely with two strains from Turkey, the Merida-like virus KE-2017a isolate 139-1-21 and the Merida-like virus Turkey isolate P431. Collectively, these results show the presence of the MERDLVT strain in Georgia.
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Affiliation(s)
| | - Adam R. Pollio
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Brian D. Knott
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Tamar Chunashvili
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Christian K. Fung
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Matthew A. Conte
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Drew D. Reinbold-Wasson
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
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Hakre S, Maljkovic-Berry I, Hang J, Conte MA, Pollio AR, Fung CK, Gandhi J, Peel SA, Lidl GM, Huhtanen ME, Hall TL, Modjarrad K, Friberg HL, O’Connell RJ, Scott PT. Transmission of SARS-CoV-2 among recruits in a US Army training environment: a brief report. J Public Health (Oxf) 2023; 45:748-752. [PMID: 37132356 PMCID: PMC10470341 DOI: 10.1093/pubmed/fdad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/10/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND In 2020, preventive measures were implemented to mitigate the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among 600-700 recruits arriving weekly at a basic combat training (BCT) facility in the southern United States. Trainees were sorted into companies and platoons (cocoons) at arrival, tested, quarantined for 14 days with daily temperature and respiratory-symptom monitoring and retested before release into larger groups for training where symptomatic testing was conducted. Nonpharmaceutical measures, such as masking, and social distancing, were maintained throughout quarantine and BCT. We assessed for SARS-CoV-2 transmission in the quarantine milieu. METHODS Nasopharyngeal (NP) swabs were collected at arrival and at the end of quarantine and blood specimens at both timepoints and at the end of BCT. Epidemiological characteristics were analyzed for transmission clusters identified from whole-genome sequencing of NP samples. RESULTS Among 1403 trainees enrolled from 25 August to 7 October 2020, epidemiological analysis identified three transmission clusters (n = 20 SARS-CoV-2 genomes) during quarantine, which spanned five different cocoons. However, SARS-CoV-2 incidence decreased from 2.7% during quarantine to 1.5% at the end of BCT; prevalence at arrival was 3.3%. CONCLUSIONS These findings suggest layered SARS-CoV-2 mitigation measures implemented during quarantine minimized the risk of further transmission in BCT.
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Affiliation(s)
- Shilpa Hakre
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Irina Maljkovic-Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Cherokee Nation Technology Solutions, Tulsa, OK, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Cherokee Nation Technology Solutions, Tulsa, OK, USA
| | - Adam R Pollio
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Cherokee Nation Technology Solutions, Tulsa, OK, USA
| | - Christian K Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Cherokee Nation Technology Solutions, Tulsa, OK, USA
| | - Jaykumar Gandhi
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Cherokee Nation Technology Solutions, Tulsa, OK, USA
| | - Sheila A Peel
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Grace M Lidl
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mark E Huhtanen
- Moncrief Army Health Clinic, Fort Jackson, Columbia, SC, USA
| | - Tara L Hall
- Moncrief Army Health Clinic, Fort Jackson, Columbia, SC, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Heather L Friberg
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Paul T Scott
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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5
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Collins ND, Beaty S, Wallace E, Li Y, Sanborn M, Yang Y, Adhikari A, Shabram P, Warfield K, Karasavvas N, Kuschner RA, Hang J. Differential Genome Replication of a Unique Single-Amino-Acid Mutation in the Adenovirus-4 Component of the Live Oral Adenovirus Type 4 and Type 7 Vaccine. Vaccines (Basel) 2023; 11:1144. [PMID: 37514960 PMCID: PMC10385111 DOI: 10.3390/vaccines11071144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
The FDA-approved Adenovirus Type 4 and Type 7 Vaccine, Live, Oral is highly effective and essential in preventing acute respiratory diseases (ARDs) in U.S. military recruits. Our study revealed the presence of a previously undetected mutation, not found in the wild-type human adenovirus type 4 (HAdV-4) component of the licensed vaccine, which contains an amino acid substitution (P388T) in the pre-terminal protein (pTP). This study demonstrated that replication of the T388 HAdV-4 vaccine mutant virus is favored over the wild type in WI-38 cells, the cell type utilized in vaccine manufacturing. However, results from serial human stool specimens of vaccine recipients support differential genome replication in the gastrointestinal tract (GI), demonstrated by the steady decline of the percentage of mutant T388 vaccine virus. Since vaccine efficacy depends upon GI replication and the subsequent immune response, the mutation can potentially impact vaccine efficacy.
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Affiliation(s)
- Natalie D Collins
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Shannon Beaty
- Emergent BioSolutions, Inc., Gaithersburg, MD 20879, USA
| | - Elana Wallace
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Yuanzhang Li
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Mark Sanborn
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Yu Yang
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Anima Adhikari
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Paul Shabram
- Emergent BioSolutions, Inc., Gaithersburg, MD 20879, USA
| | - Kelly Warfield
- Emergent BioSolutions, Inc., Gaithersburg, MD 20879, USA
| | - Nicos Karasavvas
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Robert A Kuschner
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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Beaty S, Collins N, Karasavvas N, Kuschner R, Hang J, Adhikari A, Maljkovic Berry I, Fung C, Walls S, Betancourt E, Mendy J, Lock M, Gierman E, Bennett S, Shabram P, Warfield K. A Phase 1 Two-Arm, Randomized, Double-Blind, Active-Controlled Study of Live, Oral Plasmid-Derived Adenovirus Type 4 and Type 7 Vaccines in Seronegative Adults. Vaccines (Basel) 2023; 11:1091. [PMID: 37376480 DOI: 10.3390/vaccines11061091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
PXVX0047 is an investigational vaccine developed for active immunization to prevent febrile acute respiratory disease (ARD) caused by adenovirus serotypes 4 (Ad4) and 7 (Ad7). PXVX0047 consists of a modernized, plasmid-derived vaccine that was generated using a virus isolated from Wyeth Ad4 and Ad7 vaccine tablets. A phase 1 two-arm, randomized, double-blind, active-controlled study was conducted to evaluate the safety profile and immunogenicity of the investigational adenovirus vaccines. The two components of PXVX0047 were administered orally together in a single dose to 11 subjects. For comparison, three additional subjects received the Ad4/Ad7 vaccine that is currently in use by the US military. The results of this study show that the tolerability and immunogenicity of the PXVX0047 Ad7 component are comparable with that of the control Ad4/Ad7 vaccine; however, the immunogenicity of the PXVX0047 Ad4 component was lower than expected. Clinical trial number NCT03160339.
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Affiliation(s)
- Shannon Beaty
- Emergent BioSolutions Inc., Gaithersburg, MD 20879, USA
| | - Natalie Collins
- Walter Reed Army Institute of Research, Bethesda, MD 20814, USA
| | | | - Robert Kuschner
- Walter Reed Army Institute of Research, Bethesda, MD 20814, USA
| | - Jun Hang
- Walter Reed Army Institute of Research, Bethesda, MD 20814, USA
| | - Anima Adhikari
- Walter Reed Army Institute of Research, Bethesda, MD 20814, USA
| | | | - Christian Fung
- Walter Reed Army Institute of Research, Bethesda, MD 20814, USA
| | - Shannon Walls
- Walter Reed Army Institute of Research, Bethesda, MD 20814, USA
| | | | - Jason Mendy
- Emergent BioSolutions Inc., Gaithersburg, MD 20879, USA
| | - Michael Lock
- Emergent BioSolutions Inc., Gaithersburg, MD 20879, USA
| | - Emma Gierman
- Emergent BioSolutions Inc., Gaithersburg, MD 20879, USA
| | - Sean Bennett
- Emergent BioSolutions Inc., Gaithersburg, MD 20879, USA
| | - Paul Shabram
- Emergent BioSolutions Inc., Gaithersburg, MD 20879, USA
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Ding S, Hao M, Cui Z, Wang Y, Hang J, Li X. Application of multi-SVM classifier and hybrid GSAPSO algorithm for fault diagnosis of electrical machine drive system. ISA Trans 2023; 133:529-538. [PMID: 35868910 DOI: 10.1016/j.isatra.2022.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
A method, being based on multi-class support vector machine (SVM) classifier and hybrid particle swarm optimization (PSO) and gravity search algorithm (GSA), is presented to diagnose the faults in electrical motor drive system. In this method, the global search ability of PSO and the local search ability of GSA are integrated to combine the advantages of PSO and GSA, and the multi-class SVM classifier is optimized by the hybrid GSAPSO algorithm to improve classification performance. To test the presented method, a series of simulation and experiment are studied. The diagnostic results display that the presented method can gain more precise classification accuracy than multi-class SVM with PSO and multi-class SVM with GSA.
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Affiliation(s)
- Shichuan Ding
- Anhui University, School of Electrical Engineering and Automation, China.
| | - Menglu Hao
- Anhui University, School of Electrical Engineering and Automation, China.
| | - Zhiwei Cui
- Anhui University, School of Electrical Engineering and Automation, China.
| | - Yinjiang Wang
- Anhui University, School of Electrical Engineering and Automation, China.
| | - Jun Hang
- Anhui University, School of Electrical Engineering and Automation, China.
| | - Xueyi Li
- Anhui University, School of Electrical Engineering and Automation, China.
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Pollio AR, Fries AC, Yang Y, Hughes JJ, Fung CK, Conte MA, Kuschner RA, Collins ND, Macias EA, Hang J. Clustered cases of human adenovirus types 4, 7, and 14 infections in US Department of Defense Beneficiaries during the 2018-2019 season. J Med Virol 2023; 95:e28571. [PMID: 36762593 DOI: 10.1002/jmv.28571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Human adenoviruses (HAdV) are genetically diverse and can infect a number of tissues with severities varied from mild to fatal. HAdV types 3, 4, 7, 11, 14, 21, and 55 were associated with acute respiratory illnesses outbreaks in the United States and in other countries. The risk of outbreaks can be effectively controlled by HAdV vaccination or mitigated by screening and preventive measures. During the influenza season 2018-2019, the DoD Global Respiratory Pathogen Surveillance Program (DoDGRS) received 24 300 respiratory specimens. HAdV samples that produced positive cytopathic effects in viral cultivation were subjected to next-generation sequencing for genome sequence assembly, genome typing, whole genome phylogeny, and sequence comparative analyses. A variety of HAdV types were identified in this study, including HAdV types 1-7, 14, 55, and 56. HAdV types 4, 7, and 14 were found in clustered cases in Colorado, Florida, New York, and South Carolina. Comparative sequence analyses of these isolates revealed the emergence of novel genetic mutations despite the stability of adenovirus genomes. Genomic surveillance of HAdV suggested possible undetected outbreaks and shed light on prevalence, genetic divergence, and viral evolution of HAdV. Continued surveillance will inform risk assessment and countermeasures.
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Affiliation(s)
- Adam R Pollio
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Anthony C Fries
- US Air Force School of Aerospace Medicine, Wright-Patterson AFB, Dayton, Ohio, USA
| | - Yu Yang
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jerry J Hughes
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Christian K Fung
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Matthew A Conte
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Robert A Kuschner
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Natalie D Collins
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Elizabeth A Macias
- US Air Force School of Aerospace Medicine, Wright-Patterson AFB, Dayton, Ohio, USA
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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9
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Pollio A, Fries AC, Yang Y, Hughes J, Fung C, Conte M, Collins N, Macias EA, Hang J. 2197. Genomic Surveillance for Human Adenovirus Infections among Department of Defense Beneficiaries in the 2018-2019 Season. Open Forum Infect Dis 2022. [PMCID: PMC9752949 DOI: 10.1093/ofid/ofac492.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Human adenoviruses (family Adenoviridae, genus Mastadenovirus) (HAdV) species B, C and E cause acute respiratory illnesses (ARI). In particular, respiratory HAdV types 3, 4, 7, 11, 14, 21 and 55 were associated with ARI outbreaks in the US and in other countries. The risk of outbreaks can be effectively controlled by implementation of the live HAdV types 4 and 7 vaccines or mitigated by screening and preventive measures. Methods During the influenza season 2018 – 2019, the DoD Global Respiratory Pathogen Surveillance Program (DoDGRS) received 24,300 specimens from its surveillance network. In total, 322 (1.3%) respiratory specimens were positive for HAdV in molecular assays. HAdV samples that produced positive cytopathic effects (CPE) in subsequent viral cultivation were subjected to next-gen sequencing (NGS) for genome sequence assembly, HAdV genome typing, whole genome phylogeny, and sequence comparative analyses to identify sequence insertions, deletions and amino acid mutations. Results Out of 166 viral culture samples available for NGS, whole genome sequences were obtained for 161 isolates. A variety types of HAdV were identified, including HAdV-1 (N = 15), HAdV-2 (N = 26), HAdV-3 (N = 60), HAdV-4 (N = 13), HAdV-5 (N = 6), HAdV-6 (N = 3), HAdV-7 (N = 12), HAdV-14 (N = 10), HAdV-55 (N = 1), and HAdV-56 (N = 1). HAdV types 4, 7 and 14, which were reported causing ARI outbreaks in the US military and other congregate settings, were found in clustered cases in several US states. Comparative sequence analyses of these isolates revealed the emergence of novel genetic mutations despite the stability of adenovirus genomes. Conclusion Routine clinical respiratory pathogen diagnostics or molecular surveillance of respiratory diseases detect adenovirus without determination of HAdV type. Human adenoviruses are genetically diverse and can infect a number of tissues with severities varied from mild to fatal. Enhanced genomic surveillance of HAdV in the US and worldwide will shed light on prevalence, genetic divergence, and viral evolution of human adenoviruses and inform timely risk assessment and countermeasures. Disclosures All Authors: No reported disclosures.
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Affiliation(s)
- Adam Pollio
- Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | - Jerry Hughes
- Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Christian Fung
- Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Matthew Conte
- Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Natalie Collins
- Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Elizabeth A Macias
- U.S. Air Force School of Aerospace Medicine Epidemiology Laboratory Service, Wright-Patterson AFB, Ohio
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10
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Tang CY, Boftsi M, Staudt L, McElroy JA, Li T, Duong S, Ohler A, Ritter D, Hammer R, Hang J, Wan XF. SARS-CoV-2 and influenza co-infection: A cross-sectional study in central Missouri during the 2021-2022 influenza season. Virology 2022; 576:105-110. [PMID: 36206606 PMCID: PMC9523501 DOI: 10.1016/j.virol.2022.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/15/2022] [Accepted: 09/25/2022] [Indexed: 01/16/2023]
Abstract
As SARS-CoV-2 and influenza viruses co-circulate, co-infections with these viruses generate an increasing concern to public health. To evaluate the prevalence and clinical impacts of SARS-CoV-2 and influenza A virus co-infections during the 2021-2022 influenza season, SARS-CoV-2-positive samples from 462 individuals were collected from October 2021 to January 2022. Of these individuals, 152 tested positive for influenza, and the monthly co-infection rate ranged from 7.1% to 48%. Compared to the Delta variant, individuals infected with Omicron were less likely to be co-infected and hospitalized, and individuals who received influenza vaccines were less likely to become co-infected. Three individuals had two samples collected on different dates, and all three developed a co-infection after their initial SARS-CoV-2 infection. This study demonstrates high prevalence of co-infections in central Missouri during the 2021-2022 influenza season, differences in co-infection prevalence between the Delta and the Omicron waves, and the importance of influenza vaccinations against co-infections.
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Affiliation(s)
- Cynthia Y. Tang
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA,Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Maria Boftsi
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Lindsay Staudt
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jane A. McElroy
- Family and Community Medicine, University of Missouri, Columbia, MO, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sabrina Duong
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Adrienne Ohler
- Child Health, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Detlef Ritter
- Pathology and Anatomical Sciences, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Richard Hammer
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA,Pathology and Anatomical Sciences, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, MO, USA,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA,Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA,Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA,Corresponding author. Center for Influenza and Emerging Infectious Diseases, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
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11
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Pollio AR, Jiang J, Lee SS, Gandhi JS, Knott BD, Chunashvili T, Conte MA, Walls SD, Hulseberg CE, Farris CM, Reinbold-Wasson DD, Hang J. Discovery of Rickettsia spp. in mosquitoes collected in Georgia by metagenomics analysis and molecular characterization. Front Microbiol 2022; 13:961090. [PMID: 36160204 PMCID: PMC9493313 DOI: 10.3389/fmicb.2022.961090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022] Open
Abstract
Arthropods have a broad and expanding worldwide presence and can transmit a variety of viral, bacterial, and parasite pathogens. A number of Rickettsia and Orientia species associated with ticks, fleas, lice, and mites have been detected in, or isolated from, patients with febrile illness and/or animal reservoirs throughout the world. Mosquitoes are not currently considered vectors for Rickettsia spp. pathogens to humans or to animals. In this study, we conducted a random metagenome next-generation sequencing (NGS) of 475 pools of Aedes, Culex, and Culiseta species of mosquitoes collected in Georgia from 2018 to 2019, identifying rickettsial gene sequences in 33 pools of mosquitoes. We further confirmed the findings of the Rickettsia by genus-specific quantitative PCR (qPCR) and multi-locus sequence typing (MLST). The NGS and MLST results indicate that Rickettsia spp. are closely related to Rickettsia bellii, which is not known to be pathogenic in humans. The results, together with other reports of Rickettsia spp. in mosquitoes and the susceptibility and transmissibility experiments, suggest that mosquitoes may play a role in the transmission cycle of Rickettsia spp.
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Affiliation(s)
- Adam R. Pollio
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Ju Jiang
- Naval Medical Research Center, Silver Spring, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Sam S. Lee
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Jaykumar S. Gandhi
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Brian D. Knott
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Tamar Chunashvili
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Matthew A. Conte
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Shannon D. Walls
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Christine E. Hulseberg
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | | | - Drew D. Reinbold-Wasson
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
- *Correspondence: Jun Hang,
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12
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Adenaiye OO, Lai J, Bueno de Mesquita PJ, Hong F, Youssefi S, German J, Tai SHS, Albert B, Schanz M, Weston S, Hang J, Fung C, Chung HK, Coleman KK, Sapoval N, Treangen T, Berry IM, Mullins K, Frieman M, Ma T, Milton DK. Infectious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection. Clin Infect Dis 2022; 75:e241-e248. [PMID: 34519774 PMCID: PMC8522431 DOI: 10.1093/cid/ciab797] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemiology implicates airborne transmission; aerosol infectiousness and impacts of masks and variants on aerosol shedding are not well understood. METHODS We recruited coronavirus disease 2019 (COVID-19) cases to give blood, saliva, mid-turbinate and fomite (phone) swabs, and 30-minute breath samples while vocalizing into a Gesundheit-II, with and without masks at up to 2 visits 2 days apart. We quantified and sequenced viral RNA, cultured virus, and assayed serum samples for anti-spike and anti-receptor binding domain antibodies. RESULTS We enrolled 49 seronegative cases (mean days post onset 3.8 ± 2.1), May 2020 through April 2021. We detected SARS-CoV-2 RNA in 36% of fine (≤5 µm), 26% of coarse (>5 µm) aerosols, and 52% of fomite samples overall and in all samples from 4 alpha variant cases. Masks reduced viral RNA by 48% (95% confidence interval [CI], 3 to 72%) in fine and by 77% (95% CI, 51 to 89%) in coarse aerosols; cloth and surgical masks were not significantly different. The alpha variant was associated with a 43-fold (95% CI, 6.6- to 280-fold) increase in fine aerosol viral RNA, compared with earlier viruses, that remained a significant 18-fold (95% CI, 3.4- to 92-fold) increase adjusting for viral RNA in saliva, swabs, and other potential confounders. Two fine aerosol samples, collected while participants wore masks, were culture-positive. CONCLUSIONS SARS-CoV-2 is evolving toward more efficient aerosol generation and loose-fitting masks provide significant but only modest source control. Therefore, until vaccination rates are very high, continued layered controls and tight-fitting masks and respirators will be necessary.
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Affiliation(s)
- Oluwasanmi O Adenaiye
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Jianyu Lai
- Department of Epidemiology and Biostatistics, University of Maryland School of Public Health, College Park, Maryland, USA
| | - P Jacob Bueno de Mesquita
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Filbert Hong
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Somayeh Youssefi
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Jennifer German
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - S H Sheldon Tai
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Barbara Albert
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Maria Schanz
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Christian Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Hye Kyung Chung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Kristen K Coleman
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Todd Treangen
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Kristin Mullins
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Donald K Milton
- Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
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13
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Maljkovic Berry I, Hang J, Fung C, Yang Y, Chibucos M, Pollio A, Gandhi J, Li T, Conte MA, Lidl GM, Johannigman JA, Friberg H. Genomic surveillance of SARS-CoV-2 in US military compounds in Afghanistan reveals multiple introductions and outbreaks of Alpha and Delta variants. BMC Genomics 2022; 23:513. [PMID: 35840884 PMCID: PMC9288047 DOI: 10.1186/s12864-022-08757-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
Background With the emergence and spread of SARS-CoV-2 variants, genomic epidemiology and surveillance have proven invaluable tools for variant tracking. Here, we analyzed SARS-CoV-2 samples collected from personnel located at the US/NATO bases across Afghanistan. Results Sequencing and phylogenetic analyses revealed at least 16 independent introductions of SARS-CoV-2 into four of these relatively isolated compounds during April and May 2021, including multiple introductions of Alpha and Delta variants. Four of the introductions resulted in sustained spread of the virus within, and in two cases between, the compounds. Three of these outbreaks, one Delta and two Alpha, occurred simultaneously. Conclusions Even in rigorously controlled and segregated environments, SARS-CoV-2 introduction and spread may occur frequently. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08757-5.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA.
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Christian Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Marcus Chibucos
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Adam Pollio
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Jay Gandhi
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Grace M Lidl
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Jay A Johannigman
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Heather Friberg
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
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14
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Hakre S, Lam EY, Maljkovic-Berry I, Hang J, Pow Sang LA, Bianchi EJ, Fung C, Gandhi J, Chibucos M, Conte MA, Pollio AR, Mariskanish CA, Mansfield LA, Modjarrad K, Friberg-Robertson HL, Lidl GM, Scott PT, Lougee DA. Investigation of an outbreak of COVID-19 among U.S. military personnel and beneficiaries stationed in the Republic of Korea, June-July 2021. PLOS Glob Public Health 2022; 2:e0000236. [PMID: 36962352 PMCID: PMC10021645 DOI: 10.1371/journal.pgph.0000236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/19/2022] [Indexed: 11/19/2022]
Abstract
On 28 May 2021, leisure travel restrictions in place to control coronavirus disease 2019 (COVID-19) were eased among vaccinated U.S. military personnel and beneficiaries stationed in South Korea (USFK) allowing access to bars and clubs which were off limits. We describe results from an investigation of the largest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak as of November 2021 among USFK personnel following this change in policy. Data such as SARS-CoV-2 real-time polymerase chain reaction (RT-PCR) test results, demographic characteristics, symptom and vaccination histories, and genome sequences were analyzed. Of a total 207 new cases of COVID-19 diagnosed among USFK members from 15 June to 27 July 2021, 113 (57%) eligible cases were fully vaccinated, of whom 86 (76%) were symptomatic. RT-PCR cycling threshold values were similar among vaccinated and unvaccinated members. Whole genomic sequencing of 54 outbreak samples indicated all infections were due to the Delta variant. Phylogenetic analysis revealed two sources of SARS-CoV-2 accounted for 41% of infections among vaccinated and unvaccinated members. Vaccinated personnel were not at risk of severe illness; however, 86% experienced symptoms following infection. There were no hospitalizations among COVID-19 cases, most of whom were young military service members. Rescinded restrictions were reinstated to control the outbreak. Masking was mandated among all personnel predating U.S. national recommendations for indoor masking in high COVID-19 transmission areas. Increased vaccination with continued vigilance and extension of COVID-19 mitigation measures are warranted to contain the spread of SARS-CoV-2 variants of concern.
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Affiliation(s)
- Shilpa Hakre
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Evelyn Y Lam
- United States Forces Korea, J3 -Directorate of Operations, Camp Humphreys, Pyeongtaek, South Korea
| | - Irina Maljkovic-Berry
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
- Cherokee Nation Technology Solutions, Tulsa, Oklahoma, United States of America
| | - Jun Hang
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
| | - Luis A Pow Sang
- United States Forces Korea, Brian D. Allgood Army Community Hospital, Camp Humphreys, Pyeongtaek, South Korea
| | - Elizabeth J Bianchi
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Christian Fung
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
- Cherokee Nation Technology Solutions, Tulsa, Oklahoma, United States of America
| | - Jay Gandhi
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
- Cherokee Nation Technology Solutions, Tulsa, Oklahoma, United States of America
| | - Marcus Chibucos
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
- Cherokee Nation Technology Solutions, Tulsa, Oklahoma, United States of America
| | - Matthew A Conte
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
- Cherokee Nation Technology Solutions, Tulsa, Oklahoma, United States of America
| | - Adam R Pollio
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
- Cherokee Nation Technology Solutions, Tulsa, Oklahoma, United States of America
| | - Christine A Mariskanish
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
| | - Luke A Mansfield
- United States Forces Korea, Brian D. Allgood Army Community Hospital, Camp Humphreys, Pyeongtaek, South Korea
| | - Kayvon Modjarrad
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, United States of America
| | - Heather L Friberg-Robertson
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
| | - Grace M Lidl
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, Maryland, United States of America
| | - Paul T Scott
- Walter Reed Army Institute of Research, Emerging Infectious Diseases Branch, Silver Spring, Maryland, United States of America
| | - Douglas A Lougee
- United States Forces Korea, Brian D. Allgood Army Community Hospital, Camp Humphreys, Pyeongtaek, South Korea
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15
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Sanborn MA, Wuertz KM, Kim HC, Yang Y, Li T, Pollett SD, Jarman RG, Berry IM, Klein TA, Hang J. Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea. Mol Ecol 2021; 30:5470-5487. [PMID: 34418188 DOI: 10.1111/mec.16133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022]
Abstract
Recent outbreaks of emerging and re-emerging viruses have shown that timely detection of novel arboviruses with epidemic potential is essential to mitigate human health risks. There are rising concerns that emergent JEV genotype V (GV) is circulating in Asia, against which current vaccines may not be efficacious. To ascertain if JEV GV and other arboviruses are circulating in East Asia, we conducted next-generation sequencing on 260 pools of Culex tritaeniorhynchus and Culex bitaeniorhynchus mosquitoes (6540 specimens) collected at Camp Humphreys, Republic of Korea (ROK) in 2018. Interrogation of our data revealed a highly abundant and diverse virosphere that contained sequences from 122 distinct virus species. Our statistical and hierarchical analysis uncovered correlates of potential health, virological, and ecological relevance. Furthermore, we obtained evidence that JEV GV was circulating in Pyeongtaek and, retrospectively, in Seoul in 2016 and placed these findings within the context of human and fowl reservoir activity. Sequence-based analysis of JEV GV showed a divergent genotype that is the most distant from the GIII-derived live attenuated SA14-14-2 vaccine strain and indicated regions probably responsible for reduced antibody affinity. These results emphasize recent concerns of shifting JEV genotype in East Asia and highlight the critical need for a vaccine proven efficacious against this re-emergent virus. Together, our one-health approach to Culex viral metagenomics uncovered novel insights into virus ecology and human health.
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Affiliation(s)
- Mark A Sanborn
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Heung-Chul Kim
- Force Health Protection & Preventive Medicine, US Army Medical Activity-Korea, 65th Medical Brigade, Unit #15281, APO AP 96271-5281, USA
| | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Simon D Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Terry A Klein
- Force Health Protection & Preventive Medicine, US Army Medical Activity-Korea, 65th Medical Brigade, Unit #15281, APO AP 96271-5281, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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16
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Tang CY, Wang Y, McElroy JA, Li T, Hammer R, Ritter D, Lidl GM, Webby R, Hang J, Wan XF. Reinfection with two genetically distinct SARS-CoV-2 viruses within 19 days. J Med Virol 2021; 93:5700-5703. [PMID: 34170528 PMCID: PMC8426799 DOI: 10.1002/jmv.27154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/02/2023]
Affiliation(s)
- Cynthia Y Tang
- School of Medicine, University of Missouri, Columbia, Missouri, USA.,Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Yang Wang
- School of Medicine, University of Missouri, Columbia, Missouri, USA.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Jane A McElroy
- School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Tao Li
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Richard Hammer
- School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Detlef Ritter
- School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Grace M Lidl
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Xiu-Feng Wan
- School of Medicine, University of Missouri, Columbia, Missouri, USA.,Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA.,College of Engineering, University of Missouri, Columbia, Missouri, USA
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17
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Kim HC, Jiang J, Hang J, Kim SY, Yun SM, Park CU, Kim M, Chong ST, Farris CM, Richards AL, Klein TA. Detection of Rickettsia lusitaniae Among Ornithodoros sawaii Soft Ticks Collected From Japanese Murrelet Seabird Nest Material From Gugul Island, Republic of Korea. J Med Entomol 2021; 58:1376-1383. [PMID: 33615347 DOI: 10.1093/jme/tjab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Indexed: 06/12/2023]
Abstract
In a follow-up to the investigations of soft ticks identified from seabird nest soil and litter collected from coastal islands of the Republic of Korea (ROK), Ornithodoros sawaii and Ornithodoros capensis were assessed for the presence and identification of rickettsiae. Ticks collected from samples of 50-100 g of nest litter and soil from seabird nests were identified individually by morphological techniques, and species confirmed by sequencing of the mt-rrs gene. Subsequently, tick DNA preparations were screened for the presence of rickettsiae using a genus-specific nested PCR (nPCR) assay targeting the 17 kDa antigen gene. The amplicons from the 17 kDa assay and two additional nPCR assays targeting the gltA and ompB gene fragments were sequenced and used to identify the rickettsiae. A total of 134 soft ticks belonging to two species, O. sawaii Kitaoka & Suzuki 1973 (n = 125) and O. capensis Neumann 1901 (n = 9), were collected. Rickettsia lusitaniae DNA was detected and identified among O. sawaii ticks (n = 11, 8.8%) collected from nest litter and soil of the Japanese murrelet (Synthliboramphus wumizusume Temminck 1836) at Gugul Island along the western coastal area of the ROK. This study confirmed for the first time the presence of R. lusitaniae associated with O. sawaii collected from migratory seabird nests in the ROK.
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Affiliation(s)
- Heung-Chul Kim
- Force Health Protection & Preventive Medicine, US Army Medical Activity-Korea, Unit #15281, APO AP, USA
| | - Ju Jiang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, USA
| | - Su Yeon Kim
- Pathogen Resource Management TF, National Research Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Chungbuk Province, Republic of Korea
| | - Seok-Min Yun
- Division of Arboviruses, National Institute of Health, Korea Centers for Diseases Control and Prevention, Cheongju-si, Chungbuk Province, Republic of Korea
| | - Chang-Uk Park
- Migratory Birds Research Center, Korea National Park Research Institute, Korea National Park Service, Shinan-gun, Jeonnam Province, Republic of Korea
| | - Miran Kim
- Migratory Birds Research Center, Korea National Park Research Institute, Korea National Park Service, Shinan-gun, Jeonnam Province, Republic of Korea
| | - Sung-Tae Chong
- Force Health Protection & Preventive Medicine, US Army Medical Activity-Korea, Unit #15281, APO AP, USA
| | - Christina M Farris
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - Allen L Richards
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Terry A Klein
- Force Health Protection & Preventive Medicine, US Army Medical Activity-Korea, Unit #15281, APO AP, USA
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18
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Wan XF, Tang CY, Ritter D, Wang Y, Li T, Segovia K, Kosikova M, Johnson M, Kwon HJ, Xie H, Hammer RD, McElroy JA, Hamid A, Collins ND, Hang J, Camp S. SARS-CoV-2 show no infectivity at later stages in a prolonged COVID-19 patient despite positivity in RNA testing. J Med Virol 2021; 93:4570-4575. [PMID: 33830520 PMCID: PMC8250787 DOI: 10.1002/jmv.27001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 11/08/2022]
Abstract
Inpatient coronavirus disease 2019 (COVID-19) cases present enormous costs to patients and health systems in the United States. Many hospitalized patients may continue testing COVID-19 positive even after the resolution of symptoms. Thus, a pressing concern for clinicians is the safety of discharging these asymptomatic patients if they have any remaining infectivity. This case report explores the viral viability in a patient with persistent COVID-19 over the course of a 2-month hospitalization. Positive nasopharyngeal swab samples were collected and isolated in the laboratory and analyzed by quantitative reverse-transcription polymerase chain reactions (qRT-PCR), and serology was tested for neutralizing antibodies throughout the hospitalization period. The patient experienced waning symptoms by hospital day 40 and had no viable virus growth by hospital day 41, suggesting no risk of infectivity, despite positive RT-PCR results which prolonged his hospital stay. Notably, this case showed infectivity for at least 24 days after disease onset, which is longer than the discontinuation of transmission-based precautions recommended by the Center for Disease Control and Prevention. Thus, our findings suggest that the timeline for discontinuing transmission-based precautions may need to be extended for patients with severe and prolonged COVID-19 disease. Additional large-scale studies are needed to draw definitive conclusions on the appropriate clinical management for these patients. .
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Affiliation(s)
- Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA.,Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, USA.,MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA.,MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
| | - Detlef Ritter
- Department of Pathology, University of Missouri, Columbia, Missouri, USA
| | - Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Karen Segovia
- MU Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri, USA.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Martina Kosikova
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Marc Johnson
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Hyung J Kwon
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Hang Xie
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Richard D Hammer
- Department of Pathology, University of Missouri, Columbia, Missouri, USA
| | - Jane A McElroy
- Department of Family Medicine, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Aws Hamid
- Department of Radiology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Natalie D Collins
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Simone Camp
- Department of Pathology, University of Missouri, Columbia, Missouri, USA
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19
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Fung CK, Li T, Pollett S, Alera MT, Yoon IK, Hang J, Macareo L, Srikiatkhachorn A, Ellison D, Rothman AL, Fernandez S, Jarman RG, Maljkovic Berry I. Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies. J Gen Virol 2021; 102:001553. [PMID: 33591246 PMCID: PMC8515859 DOI: 10.1099/jgv.0.001553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022] Open
Abstract
Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loads, there might not be enough genetic material for deep sequencing and iSNV determination. Isolation of the virus from clinical samples with low-passage number increases viral load, but few studies have investigated how dengue virus (DENV) culture isolation from a clinical sample impacts the consensus sequence and the intra-host virus population frequencies. In this study, we investigate consensus and iSNV frequency differences between DENV sequenced directly from clinical samples and their corresponding low-passage isolates. Twenty five DENV1 and DENV2 positive sera and their corresponding viral isolates (T. splendens inoculation and C6/36 passage) were obtained from a prospective cohort study in the Philippines. These were sequenced on MiSeq with minimum nucleotide depth of coverage of 500×, and iSNVs were detected using LoFreq. For both DENV1 and DENV2, we found a maximum of one consensus nucleotide difference between clinical sample and isolate. Interestingly, we found that iSNVs with frequencies ≥5 % were often preserved between the samples, and that the number of iSNV positions, and sample diversity, at this frequency cutoff did not differ significantly between the sample pairs (clinical sample and isolate) in either DENV1 or DENV2 data. Our results show that low-passage DENV isolate consensus genomes are largely representative of their direct sample parental viruses, and that low-passage isolates often mirror high frequency within-host variants from direct samples.
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Affiliation(s)
| | - Tao Li
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Simon Pollett
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - In-Kyu Yoon
- Coalition for Epidemic Preparedness Innovations, Washington, DC, USA
| | - Jun Hang
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Louis Macareo
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anon Srikiatkhachorn
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- University of Rhode Island, Kingston, RI, USA
| | - Damon Ellison
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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20
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Liu W, Kizu JR, Matley DR, Grant R, McCallum FJ, Moller CG, Carthew TL, Hang J, Gubala AJ, Aaskov JG. Circulation of 2 Barmah Forest Virus Lineages in Military Training Areas, Australia. Emerg Infect Dis 2020; 26:3061-3065. [PMID: 33219791 PMCID: PMC7706964 DOI: 10.3201/eid2612.191747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
During 2017–2018, Barmah Forest virus was recovered from mosquitoes trapped in military training areas in Australia and from a soldier infected at 1 of these areas. Phylogenies of the nucleotide sequences of the envelope glycoprotein gene E2 and the 3′ untranslated region suggest that 2 lineages are circulating in eastern Australia.
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21
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Collins ND, Adhikari A, Yang Y, Kuschner RA, Karasavvas N, Binn LN, Walls SD, Graf PCF, Myers CA, Jarman RG, Hang J. Live Oral Adenovirus Type 4 and Type 7 Vaccine Induces Durable Antibody Response. Vaccines (Basel) 2020; 8:vaccines8030411. [PMID: 32718082 PMCID: PMC7564809 DOI: 10.3390/vaccines8030411] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 11/26/2022] Open
Abstract
Human adenoviruses (AdV) are mostly associated with minimal pathology. However, more severe respiratory tract infections and acute respiratory diseases, most often caused by AdV-4 and AdV-7, have been reported. The only licensed vaccine in the United States, live oral AdV-4 and AdV-7 vaccine, is indicated for use in the military, nearly exclusively in recruit populations. The excellent safety profile and prominent antibody response of the vaccine is well established by placebo-controlled clinical trials, while, long-term immunity of vaccination has not been studied. Serum samples collected over 6 years from subjects co-administered live oral AdV-4 and AdV-7 vaccine in 2011 were evaluated to determine the duration of the antibody response. Group geometric mean titers (GMT) at 6 years post vaccination compared to previous years evaluated were not significantly different for either AdV-4 or AdV-7 vaccine components. There were no subjects that demonstrated waning neutralization antibody (NAb) titers against AdV-4 and less than 5% of subjects against AdV-7. Interestingly, there were subjects that had a four-fold increase in NAb titers against either AdV-4 or AdV-7, at various time points post vaccination, suggesting either homotypic or heterotypic re-exposure. This investigation provided strong evidence that the live oral AdV-4 and AdV-7 vaccine induced long-term immunity to protect from AdV-4 and AdV-7 infections.
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Affiliation(s)
- Natalie D. Collins
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
- Correspondence: ; Tel.: +1-301-319-3062
| | - Anima Adhikari
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
| | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
| | - Robert A. Kuschner
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
| | - Nicos Karasavvas
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
| | - Leonard N. Binn
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
| | - Shannon D. Walls
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
| | - Paul C. F. Graf
- Naval Health Research Center, San Diego, CA 92186, USA; (P.C.F.G.); (C.A.M.)
- U.S. Navy Medical Research Unit Six, Lima 07006, Peru
| | | | - Richard G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, MD 20910, USA; (A.A.); (Y.Y.); (R.A.K.); (N.K.); (L.N.B.); (S.D.W.); (R.G.J.); (J.H.)
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22
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Hang J, Kajon AE, Graf PCF, Berry IM, Yang Y, Sanborn MA, Fung CK, Adhikari A, Balansay-Ames MS, Myers CA, Binn LN, Jarman RG, Kuschner RA, Collins ND. Human Adenovirus Type 55 Distribution, Regional Persistence, and Genetic Variability. Emerg Infect Dis 2020; 26:1497-1505. [PMID: 32568062 PMCID: PMC7323512 DOI: 10.3201/eid2607.191707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human adenovirus type 55 (HAdV-55) causes acute respiratory disease of variable severity and has become an emergent threat in both civilian and military populations. HAdV-55 infection is endemic to China and South Korea, but data from other regions and time periods are needed for comprehensive assessment of HAdV-55 prevalence from a global perspective. In this study, we subjected HAdV-55 isolates from various countries collected during 1969-2018 to whole-genome sequencing, genomic and proteomic comparison, and phylogenetic analyses. The results show worldwide distribution of HAdV-55; recent strains share a high degree of genomic homogeneity. Distinct strains circulated regionally for several years, suggesting persistent local transmission. Several cases of sporadic introduction of certain strains to other countries were documented. Among the identified amino acid mutations distinguishing HAdV-55 strains, some have potential impact on essential viral functions and may affect infectivity and transmission.
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23
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Keiser P, Kosisky S, Marks M, Reese B, Maas K, O'Neill R, Hang J. Correlation of atmospheric mold with the upper airway mycobiomes of healthy volunteers. J Allergy Clin Immunol 2020. [DOI: 10.1016/j.jaci.2019.12.335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Rothan HA, Zhong Y, Sanborn MA, Teoh TC, Ruan J, Yusof R, Hang J, Henderson MJ, Fang S. Small molecule grp94 inhibitors block dengue and Zika virus replication. Antiviral Res 2019; 171:104590. [PMID: 31421166 DOI: 10.1016/j.antiviral.2019.104590] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/06/2019] [Accepted: 08/13/2019] [Indexed: 12/20/2022]
Abstract
Two major flaviviruses, dengue virus (DENV) and Zika virus (ZIKV), cause severe health and economic burdens worldwide. Recently, genome-wide screenings have uncovered the importance of regulators of the Hrd1 ubiquitin ligase-mediated endoplasmic reticulum (ER)-associated degradation (ERAD) pathway for flavivirus replication in host cells. Here we report the identification of the compound Bardoxolone methyl (CDDO-me) as a potent inhibitor of the Hrd1 ubiquitin ligase-mediated ERAD, which possesses a broad-spectrum activity against both DENV and ZIKV. Cellular thermal shift assay (CETSA) suggested that CDDO-me binds to grp94, a key component of the Hrd1 pathway, at a low nanomolar concentration, whereas interaction was not detected with its paralog Hsp90. CDDO-me and the grp94 inhibitor PU-WS13 substantially suppressed DENV2 replication and the cytopathic effects caused by DENV and ZIKV infection. The antiviral activities of both compounds were demonstrated for all four DENV serotypes and four ZIKV strains in multiple human cell lines. This study defines grp94 as a crucial host factor for flavivirus replication and identified CDDO-me as a potent small molecule inhibitor of flavivirus infection. Inhibition of grp94 may contribute to the antiviral activity of CDDO-me. Further investigation of grp94 inhibitors may lead to a new class of broad-spectrum anti-flaviviral medications.
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Affiliation(s)
- Hussin A Rothan
- Center for Biomedical Engineering and Technology, Department of Physiology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yongwang Zhong
- Center for Biomedical Engineering and Technology, Department of Physiology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Mark A Sanborn
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Teow Chong Teoh
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Jingjing Ruan
- Center for Biomedical Engineering and Technology, Department of Physiology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Rohana Yusof
- Department of Molecular Medicine, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Shengyun Fang
- Center for Biomedical Engineering and Technology, Department of Physiology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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25
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Zhang Y, Xiang J, Han Y, Huang M, Hang J, Abbas AE, Li H. Initial experience of robot-assisted Ivor-Lewis esophagectomy: 61 consecutive cases from a single Chinese institution. Dis Esophagus 2018; 31:5032891. [PMID: 29873693 DOI: 10.1093/dote/doy048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This study aims to report the technical details and preliminary outcomes of robot-assisted Ivor-Lewis esophagectomy (RAILE) using two different types of intrathoracic anastomosis from a single institution in China. From May 2015 to October 2017, 61 patients diagnosed with mid-lower esophageal cancer were treated with RAILE. The RAILE procedure was performed in two stages. The first 35 patients underwent circular end-to-end stapled intrathoracic anastomosis (stapled group), and the remaining 26 patients had a double-layered, completely hand-sewn intrathoracic anastomosis (hand-sewn group). Patient characteristics, surgical techniques, postoperative complications, and pathology outcomes were analyzed. The mean operating time and mean blood loss were 315.6 ± 59.4 minutes and 189.3 ± 95.8 mL, respectively. There was one patient who underwent conversion to thoracotomy. The 30-day and in-hospital mortality rates were 0%. Overall complications were observed in 22 patients (36.1%) according to the Clavien-Dindo (CD) and the Esophagectomy Complications Consensus Group (ECCG) classifications, of whom 6 patients (9.8%) had anastomotic leakage (ECCG, Type II). The median length of hospitalization (LOH) was 10 days (IQR, 5 days). Complete (R0) resection was achieved in all cases. The mean tumor size was 3.2 ± 1.5 cm, and the mean number of totally dissected lymph nodes was 19.3 ± 9.2. Regarding the operative outcomes between stapled and hand-sewn groups, there were no significant differences in the operative time (325.4 ± 66.6 vs. 302.3 ± 45.9 min, P = 0.114), blood loss (172.9 ± 74.1 vs. 211.5 ± 117.0 mL, P = 0.147), conversion rate (2.9 vs. 0%, P = 1.000), overall complication rate (37.1 vs. 34.6%, P = 0.839) or LOH (10 vs. 9.5 days, P = 0.415). RAILE using both stapled and hand-sewn intrathoracic anastomosis is safe and technically feasible with satisfactory perioperative outcomes for the treatment of mid-lower thoracic esophageal cancer.
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Affiliation(s)
- Y Zhang
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - J Xiang
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Y Han
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - M Huang
- Department of Epidemiology, MD Anderson Cancer Center, University of Texas, Houston, Texas
| | - J Hang
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - A E Abbas
- Department of Thoracic Medicine and Surgery, Temple University Health System, Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - H Li
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Castillo Oré RM, Caceda RE, Huaman AA, Williams M, Hang J, Juarez DE, Kochel TJ, Halsey ES, Forshey BM. Molecular and antigenic characterization of group C orthobunyaviruses isolated in Peru. PLoS One 2018; 13:e0200576. [PMID: 30024910 PMCID: PMC6053143 DOI: 10.1371/journal.pone.0200576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 07/01/2018] [Indexed: 11/30/2022] Open
Abstract
Group C orthobunyaviruses (GRCVs) are a complex of viruses in the genus Orthobunyavirus and are associated with human febrile disease in tropical and subtropical areas of South and Central America. While numerous GRCVs have been isolated from mosquitoes, animals, and humans, genetic analysis of these viruses is limited. In this study, we characterized 65 GRCV isolates from febrile patients identified through clinic-based surveillance in the northern and southern Peruvian Amazon. A 500 base pair region of the S segment and 750 base pair regions of the M and L segments were sequenced. Pairwise sequence analysis of the clinical isolates showed nucleotide identities ranging from 68% to 100% and deduced amino acid sequence identities ranging from 72% to 100%. Sequences were compared with reference strains of the following GRCVs: Caraparu virus (CARV), Murutucu virus (MURV), Oriboca virus (ORIV), Marituba virus (MTBV), Itaqui virus (ITQV), Apeu virus (APEUV), and Madrid virus (MADV). Sequence comparison of clinical isolates with the prototype strains based on the S and L segments identified two clades; clade I included isolates with high genetic association with CARV-MADV, and clade II included isolates with high genetic association with MURV, ORIV, APEUV, and MTBV. Genetic relationships based on the M segment were at time inconsistent with those based on the S and L segments. However, clade groupings based on the M segment were highly consistent with relationships based on microneutralization assays. These results advance our understanding of the genetic and serologic relationships of GRCVs circulating in the Peruvian Amazon.
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Affiliation(s)
| | | | | | - Maya Williams
- U.S. Naval Medical Research Center, Silver Spring, Maryland, United States of America
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Diana E. Juarez
- U.S. Naval Medical Research Unit No. 6, Iquitos and Lima, Peru
| | | | - Eric S. Halsey
- U.S. Naval Medical Research Unit No. 6, Iquitos and Lima, Peru
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Binn LN, Norby EA, Marchwicki RH, Jarman RG, Keiser PB, Hang J. Canine caliciviruses of four serotypes from military and research dogs recovered in 1963-1978 belong to two phylogenetic clades in the Vesivirus genus. Virol J 2018; 15:39. [PMID: 29471848 PMCID: PMC5824495 DOI: 10.1186/s12985-018-0944-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/02/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vesiviruses (family Caliciviridae) had been shown capable of invading a variety of host species, raising concern of their zoonotic potential. Since the 1980's, several canine caliciviruses (CaCV) isolates have been reported and are phylogenetically related to the vesiviruses with features distinct from both Vesicular exanthema of swine virus (VESV) and Feline calicivirus (FCV) species in phylogeny, serology and cell culture specificities. Etiological studies of canine diseases in dogs used for military services and laboratory studies were conducted in 1963-1978 at the Walter Reed Army Institute of Research. Multiple known and unknown viral pathogens including caliciviruses were recovered. METHODS Four unidentified isolates were recovered in Walter Reed Canine Cells (WRCC) from respiratory, fecal and penile specimens. Physicochemical tests, electron microscopy, viral cultivation in human and animal cells, antibody neutralization assays, and recently the genome sequencing were used to characterize the isolates. Sera from these dogs and their cohorts were tested with the isolates to determine origin and prevalence of the infections. RESULTS The viral isolates were small non-enveloped spherical RNA virions, 27 to 42 nm in diameter with cup-like structures, indicating they are caliciviruses. They propagated in WRCC and MDCK cells, not in either other canine cells or human and other animal cells. Each isolate is antigenically distinct and react with dog sera in respective cohorts. The genomes have nucleotide identities ranging from 70.3% to 90.7% and encode the non-structural polyprotein (1810 amino acids), major capsid protein (691 amino acids) and minor structural protein (134 amino acids). They belong to two different phylogenetic clades in Vesivirus genus with close relation with canine calicivirus (CaCV). CONCLUSIONS These CaCV isolates have restricted cell tropism, antigenic diversity and genetic variation. Further investigation will shed light on antigenic relation to other vesiviruses, and its pathogenicity for dogs and potential infectivity to other animals. Together with the previously reported CaCV strains provides significant evidence to support the formation of a new CaCV species in the Vesivirus genus.
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Affiliation(s)
- Leonard N Binn
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
| | - Erica A Norby
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Ruth H Marchwicki
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Paul B Keiser
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
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Mullins KE, Hang J, Clifford RJ, Onmus-Leone F, Yang Y, Jiang J, Leguia M, Kasper MR, Maguina C, Lesho EP, Jarman RG, Richards A, Blazes D. Whole-Genome Analysis of Bartonella ancashensis, a Novel Pathogen Causing Verruga Peruana, Rural Ancash Region, Peru. Emerg Infect Dis 2018; 23:430-438. [PMID: 28221130 PMCID: PMC5382735 DOI: 10.3201/eid2303.161476] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The genus Bartonella contains >40 species, and an increasing number of these Bartonella species are being implicated in human disease. One such pathogen is Bartonella ancashensis, which was isolated in blood samples from 2 patients living in Caraz, Peru, during a clinical trial of treatment for bartonellosis. Three B. ancashensis strains were analyzed by using whole-genome restriction mapping and high-throughput pyrosequencing. Genome-wide comparative analysis of Bartonella species showed that B. ancashensis has features seen in modern and ancient lineages of Bartonella species and is more related to B. bacilliformis. The divergence between B. ancashensis and B. bacilliformis is much greater than what is seen between known Bartonella genetic lineages. In addition, B. ancashensis contains type IV secretion system proteins, which are not present in B. bacilliformis. Whole-genome analysis indicates that B. ancashensis might represent a distinct Bartonella lineage phylogenetically related to B. bacilliformis.
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Hang J, Zavaljevski N, Yang Y, Desai V, Ruck RC, Macareo LR, Jarman RG, Reifman J, Kuschner RA, Keiser PB. Composition and variation of respiratory microbiota in healthy military personnel. PLoS One 2017; 12:e0188461. [PMID: 29216202 PMCID: PMC5720755 DOI: 10.1371/journal.pone.0188461] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 11/07/2017] [Indexed: 01/16/2023] Open
Abstract
Certain occupational and geographical exposures have been associated with an increased risk of lung disease. As a baseline for future studies, we sought to characterize the upper respiratory microbiomes of healthy military personnel in a garrison environment. Nasal, oropharyngeal, and nasopharyngeal swabs were collected from 50 healthy active duty volunteers eight times over the course of one year (1107 swabs, completion rate = 92.25%) and subjected to pyrosequencing of the V1–V3 region of 16S rDNA. Respiratory bacterial taxa were characterized at the genus level, using QIIME 1.8 and the Ribosomal Database Project classifier. High levels of Staphylococcus, Corynebacterium, and Propionibacterium were observed among both nasal and nasopharyngeal microbiota, comprising more than 75% of all operational taxonomical units (OTUs). In contrast, Streptococcus was the sole dominant bacterial genus (approximately 50% of all OTUs) in the oropharynx. The average bacterial diversity was greater in the oropharynx than in the nasal or nasopharyngeal region at all time points. Diversity analysis indicated a significant overlap between nasal and nasopharyngeal samples, whereas oropharyngeal samples formed a cluster distinct from these two regions. The study produced a large set of pyrosequencing data on the V1–V3 region of bacterial 16S rDNA for the respiratory microbiomes of healthy active duty Service Members. Pre-processing of sequencing reads showed good data quality. The derived microbiome profiles were consistent both internally and with previous reports, suggesting their utility for further analyses and association studies based on sequence and demographic data.
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Affiliation(s)
- Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Nela Zavaljevski
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Valmik Desai
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Richard C. Ruck
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Louis R. Macareo
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Richard G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Robert A. Kuschner
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Paul B. Keiser
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
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Maina AN, Klein TA, Kim HC, Chong ST, Yang Y, Mullins K, Jiang J, St. John H, Jarman RG, Hang J, Richards AL. Molecular characterization of novel mosquito-borne Rickettsia spp. from mosquitoes collected at the Demilitarized Zone of the Republic of Korea. PLoS One 2017; 12:e0188327. [PMID: 29155880 PMCID: PMC5695765 DOI: 10.1371/journal.pone.0188327] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/03/2017] [Indexed: 12/21/2022] Open
Abstract
Rickettsiae are associated with a diverse range of invertebrate hosts. Of these, mosquitoes could emerge as one of the most important vectors because of their ability to transmit significant numbers of pathogens and parasites throughout the world. Recent studies have implicated Anopheles gambiae as a potential vector of Rickettsia felis. Herein we report that a metagenome sequencing study identified rickettsial sequence reads in culicine mosquitoes from the Republic of Korea. The detected rickettsiae were characterized by a genus-specific quantitative real-time PCR assay and sequencing of rrs, gltA, 17kDa, ompB, and sca4 genes. Three novel rickettsial genotypes were detected (Rickettsia sp. A12.2646, Rickettsia sp. A12.2638 and Rickettsia sp. A12.3271), from Mansonia uniformis, Culex pipiens, and Aedes esoensis, respectively. The results underscore the need to determine the Rickettsia species diversity associated with mosquitoes, their evolution, distribution and pathogenic potential.
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Affiliation(s)
- Alice N. Maina
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Terry A. Klein
- 65 Medical Brigade, Medical Department Activity-Korea, Unit 15281, Seoul, South Korea
| | - Heung-Chul Kim
- 65 Medical Brigade, Medical Department Activity-Korea, Unit 15247, Seoul, South Korea
| | - Sung-Tae Chong
- 65 Medical Brigade, Medical Department Activity-Korea, Unit 15247, Seoul, South Korea
| | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Kristin Mullins
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- University of Maryland, School of Medicine, Department of Pathology, Baltimore, Maryland, United States of America
| | - Ju Jiang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
| | - Heidi St. John
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
| | - Richard G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Allen L. Richards
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
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Hang J, Vento TJ, Norby EA, Jarman RG, Keiser PB, Kuschner RA, Binn LN. Adenovirus type 4 respiratory infections with a concurrent outbreak of coxsackievirus A21 among United States Army Basic Trainees, a retrospective viral etiology study using next-generation sequencing. J Med Virol 2017; 89:1387-1394. [PMID: 28198541 DOI: 10.1002/jmv.24792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/30/2017] [Indexed: 11/09/2022]
Abstract
Human adenoviruses (HAdV), in particular types 4 and 7, frequently cause acute respiratory disease (ARD) during basic military training. HAdV4 and HAdV7 vaccines reduced the ARD risk in U.S. military. It is important to identify other respiratory pathogens and assess their potential impact on military readiness. In 2002, during a period when the HAdV vaccines were not available, throat swabs were taken from trainees (n = 184) with respiratory infections at Fort Jackson, South Carolina. Viral etiology was investigated initially with viral culture and neutralization assay and recently in this study by sequencing the viral isolates. Viral culture and neutralization assays identified 90 HAdV4 isolates and 27 additional cultures that showed viral cytopathic effects (CPE), including some with picornavirus-like CPE. Next-generation sequencing confirmed these results and determined viral genotypes, including 77 HAdV4, 4 HAdV3, 1 HAdV2, 17 coxsackievirus A21 (CAV21), and 1 enterovirus D68. Two samples were positive for both HAdV4 and CAV21. The identified genotypes are phylogenetically close to but distinct from those found during other years or in other military/non-military sites. HAdV4 is the predominant respiratory pathogen in unvaccinated military trainee. HAdV4 has temporal and demographic variability. CAV21 is a significant respiratory pathogen and needs to be evaluated for its current significance in military basic trainees.
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Affiliation(s)
- Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Todd J Vento
- Preventive Medicine Department, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Erica A Norby
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Paul B Keiser
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Robert A Kuschner
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Leonard N Binn
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Xiao YZ, Chen Q, Hang J, Shi YY, Xiao YZ, Wu J, Hong YZ, Wang YP. Selective induction, purification and characterization of a laccase isozyme from the basidiomyceteTrametessp. AH28-2. Mycologia 2017. [DOI: 10.1080/15572536.2005.11832993] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | - Y. Y. Shi
- Laboratory of Structure Biology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. of China
| | | | | | | | - Y. P. Wang
- Laboratory of Microorganism and Gene Technology, School of Life Sciences, Anhui University, Hefei, Anhui, 230039, P.R. of China
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Maina AN, Luce-Fedrow A, Omulo S, Hang J, Chan TC, Ade F, Jima DD, Ogola E, Ge H, Breiman RF, Njenga MK, Richards AL. Isolation and characterization of a novel Rickettsia species (Rickettsia asembonensis sp. nov.) obtained from cat fleas (Ctenocephalides felis). Int J Syst Evol Microbiol 2016; 66:4512-4517. [DOI: 10.1099/ijsem.0.001382] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Alice N. Maina
- Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Alison Luce-Fedrow
- Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
- Shippensburg University, 1871 Old Main Drive, Shippensburg, PA 17257, USA
| | | | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Teik-Chye Chan
- Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | | | - Dereje D. Jima
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Eric Ogola
- Kenya Medical Research Institute, Kisumu, Kenya
| | - Hong Ge
- Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | | | | | - Allen L. Richards
- Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
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Zhou Y, Fernandez S, Yoon IK, Simasathien S, Watanaveeradej V, Yang Y, Marte-Salcedo OA, Shuck-Lee DJ, Thomas SJ, Hang J, Jarman RG. Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens and Identification of Human Enteroviruses at a Thailand Hospital. Am J Trop Med Hyg 2016; 95:663-669. [PMID: 27352877 PMCID: PMC5014275 DOI: 10.4269/ajtmh.16-0062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/12/2016] [Indexed: 12/11/2022] Open
Abstract
Numerous pathogens cause respiratory infections with similar symptoms. Routine diagnostics detect only a limited number of pathogens, leaving a gap in respiratory illness etiology surveillance. This study evaluated next-generation sequencing for unbiased pathogen identification. Respiratory samples collected in Thailand, Philippines, Bhutan, and Nepal, that were negative by several molecular and immunofluorescence assays, underwent viral cultivation. Samples which demonstrated cytopathic effect in culture (N = 121) were extracted and tested by Luminex xTAG respiratory viral panel (RVP) assay and deep sequencing by Roche 454 FLX Titanium system. Using RVP assay, 52 (43%) samples were positive for enterovirus or rhinovirus and another three were positive for respiratory syncytial virus B, parainfluenza 4, and adenovirus. Deep sequencing confirmed the Luminex assay results and identified additional viral pathogens. Human enteroviruses, including Enterovirus A type 71 and 12 types of Enterovirus B (EV-B) were identified from a hospital in Bangkok. Phylogenetic and recombination analysis showed high correlation of VP1 gene-based phylogeny with genome-wide phylogeny and the frequent genetic exchange among EV-B viruses. The high number and diversity of enteroviruses in the hospital in Bangkok suggests prevalent existence. The metagenomic approach used in our study enabled comprehensive diagnoses of respiratory viruses.
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Affiliation(s)
- Yanfei Zhou
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Stefan Fernandez
- Department of Virology, U.S. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - In-Kyu Yoon
- International Vaccine Institute, Seoul, Republic of Korea.,Department of Virology, U.S. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Omely A Marte-Salcedo
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Deidra J Shuck-Lee
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Stephen J Thomas
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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35
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Mullins KE, Hang J, Jiang J, Leguia M, Kasper MR, Ventosilla P, Maguiña C, Jarman RG, Blazes D, Richards AL. Description of Bartonella ancashensis sp. nov., isolated from the blood of two patients with verruga peruana. Int J Syst Evol Microbiol 2015; 65:3339-3343. [DOI: 10.1099/ijsem.0.000416] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel isolates of the genus Bartonella were recovered from the blood of two patients enrolled in a clinical trial for the treatment of chronic stage Bartonella bacilliformis infection (verruga peruana) in Caraz, Ancash, Peru. The isolates were initially characterized by sequencing a fragment of the gltA gene, and found to be disparate from B. bacilliformis. The isolates were further characterized using phenotypic and genotypic methods, and found to be genetically identical to each other for the genes assessed, but distinct from any known species of the genus Bartonella, including the closest relative B. bacilliformis. Other characteristics of the isolates, including their morphology, microscopic and biochemical properties, and growth patterns, were consistent with members of the genus Bartonella. Based on these results, we conclude that these three isolates are members of a novel species of the genus Bartonella for which we propose the name Bartonella ancashensis sp. nov. (type strain 20.00T = ATCC BAA-2694T = DSM 29364T).
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Affiliation(s)
- Kristin E. Mullins
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- U.S. Naval Medical Research Center, Silver Spring, MD 20910, USA
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Ju Jiang
- U.S. Naval Medical Research Center, Silver Spring, MD 20910, USA
| | | | | | - Palmira Ventosilla
- Instituto de Medicina Tropical Alexander von Humboldt-Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ciro Maguiña
- Instituto de Medicina Tropical Alexander von Humboldt-Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Richard G. Jarman
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - David Blazes
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Allen L. Richards
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- U.S. Naval Medical Research Center, Silver Spring, MD 20910, USA
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Yang Y, Garver LS, Bingham KM, Hang J, Jochim RC, Davidson SA, Richardson JH, Jarman RG. Feasibility of Using the Mosquito Blood Meal for Rapid and Efficient Human and Animal Virus Surveillance and Discovery. Am J Trop Med Hyg 2015; 93:1377-82. [PMID: 26416112 DOI: 10.4269/ajtmh.15-0440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/03/2015] [Indexed: 11/07/2022] Open
Abstract
Mosquito blood meals taken from humans and animals potentially represent a useful source of blood for the detection of blood-borne pathogens. In this feasibility study, Anopheles stephensi mosquitoes were fed with blood meals spiked with dengue virus type 2 (DENV-2) and harvested at serial time points. These mosquitoes are not competent vectors, and the virus is not expected to replicate. Ingested blood was spotted on Whatman FTA cards and stored at room temperature. Mosquito abdomens were removed and stored at -80°C. Control blood meal aliquots were stored in vials or applied onto FTA cards. After 4 weeks of storage, the samples were extracted using beadbeating and QIAamp Viral RNA kit (Qiagen Sciences, Germantown, MD). Recovered viral RNA was analyzed by DENV-2 TaqMan RT-PCR assay and next-generation sequencing (NGS). Overall viral RNA recovery efficiency was 15% from the directly applied dried blood spots and approximately 20% or higher for dried blood spots made by blotting mosquito midgut on FTA cards. Viral RNA in mosquito-ingested blood decreases over time, but remains detectable 24 hours after blood feeding. The viral sequences in FTA-stored specimens can be maintained at room temperature. The strategy has the potential utility in expedited zoonotic virus discovery and blood-borne pathogen surveillance.
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Affiliation(s)
- Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Lindsey S Garver
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Karen M Bingham
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Ryan C Jochim
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Silas A Davidson
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jason H Richardson
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland; Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Kajon AE, Hang J, Hawksworth A, Metzgar D, Hage E, Hansen CJ, Kuschner RA, Blair P, Russell KL, Jarman RG. Molecular Epidemiology of Adenovirus Type 21 Respiratory Strains Isolated From US Military Trainees (1996-2014). J Infect Dis 2015; 212:871-80. [PMID: 25748322 DOI: 10.1093/infdis/jiv141] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/27/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The circulation of human adenovirus type 21 (HAdV21) in the United States has been documented since the 1960s in association with outbreaks of febrile respiratory illness (FRI) in military boot camps and civilian cases of respiratory disease. METHODS To describe the molecular epidemiology of HAdV21 respiratory infections across the country, 150 clinical respiratory isolates obtained from continuous surveillance of military recruit FRI, and 23 respiratory isolates recovered from pediatric and adult civilian cases of acute respiratory infection were characterized to compile molecular typing data spanning 37 years (1978-2014). RESULTS Restriction enzyme analysis and genomic sequencing identified 2 clusters of closely related genomic variants readily distinguishable from the prototype and designated 21a-like and 21b-like. A-like variants predominated until 1999. A shift to b-like variants was noticeable by 2007 after a 7-year period (2000-2006) of cocirculation of the 2 genome types. US strains are phylogenetically more closely related to European and Asian strains isolated over the last 4 decades than to the Saudi Arabian prototype strain AV-1645 isolated in 1956. CONCLUSIONS Knowledge of circulating HAdV21 variants and their epidemic behavior will be of significant value to local and global FRI surveillance efforts.
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Affiliation(s)
- Adriana E Kajon
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Anthony Hawksworth
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, California
| | - David Metzgar
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, California
| | - Elias Hage
- Institute of Virology, Hannover Medical School, Germany
| | - Christian J Hansen
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, California
| | - Robert A Kuschner
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Patrick Blair
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, California
| | - Kevin L Russell
- Armed Forces Health Surveillance Center, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Farlow J, Filippov AA, Sergueev KV, Hang J, Kotorashvili A, Nikolich MP. Comparative whole genome analysis of six diagnostic brucellaphages. Gene 2014; 541:115-22. [PMID: 24530704 DOI: 10.1016/j.gene.2014.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/04/2013] [Accepted: 01/07/2014] [Indexed: 11/24/2022]
Abstract
Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic comparisons including recently described genomes of the Tb phage from Mexico (TbM) and Pr phage to elucidate genomic diversity and candidate host range determinants. Comparative whole genome analysis revealed high sequence homogeneity among these brucellaphage genomes and resolved three genetic groups consistent with defined host range phenotypes. Group I was composed of Tb and Fz phages that are predominantly lytic for Brucella abortus and Brucella neotomae; Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus, Brucella melitensis and Brucella suis; Group III was composed of Wb and S708 phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the putative phage collar protein is a variable locus with features that may be contributing to the host specificities exhibited by different brucellaphage groups. The presence of several candidate host range determinants is illustrated herein for future dissection of the differential host specificity observed among these phages.
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Affiliation(s)
| | - Andrey A Filippov
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kirill V Sergueev
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Adam Kotorashvili
- Richard G. Lugar Center for Public Health Research, Tbilisi, Georgia
| | - Mikeljon P Nikolich
- Department of Emerging Bacterial Infections, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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39
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Hang J, Desai V, Zavaljevski N, Yang Y, Lin X, Satya RV, Martinez LJ, Blaylock JM, Jarman RG, Thomas SJ, Kuschner RA. 16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles. Microbiome 2014; 2:31. [PMID: 25228989 PMCID: PMC4165438 DOI: 10.1186/2049-2618-2-31] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/29/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Sample storage conditions, extraction methods, PCR primers, and parameters are major factors that affect metagenomics analysis based on microbial 16S rRNA gene sequencing. Most published studies were limited to the comparison of only one or two types of these factors. Systematic multi-factor explorations are needed to evaluate the conditions that may impact validity of a microbiome analysis. This study was aimed to improve methodological options to facilitate the best technical approaches in the design of a microbiome study. Three readily available mock bacterial community materials and two commercial extraction techniques, Qiagen DNeasy and MO BIO PowerSoil DNA purification methods, were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing-based analysis. Primers were chosen for 16S rDNA quantitative PCR and amplification of region V3 to V1. Swabs spiked with mock bacterial community cells and clinical oropharyngeal swabs were incubated at respective temperatures of -80°C, -20°C, 4°C, and 37°C for 4 weeks, then extracted with the two methods, and subjected to pyrosequencing and taxonomic and statistical analyses to investigate microbiome profile stability. RESULTS The bacterial compositions for the mock community DNA samples determined in this study were consistent with the projected levels and agreed with the literature. The quantitation accuracy of abundances for several genera was improved with changes made to the standard Human Microbiome Project (HMP) procedure. The data for the samples purified with DNeasy and PowerSoil methods were statistically distinct; however, both results were reproducible and in good agreement with each other. The temperature effect on storage stability was investigated by using mock community cells and showed that the microbial community profiles were altered with the increase in incubation temperature. However, this phenomenon was not detected when clinical oropharyngeal swabs were used in the experiment. CONCLUSIONS Mock community materials originated from the HMP study are valuable controls in developing 16S metagenomics analysis procedures. Long-term exposure to a high temperature may introduce variation into analysis for oropharyngeal swabs, suggestive of storage at 4°C or lower. The observed variations due to sample storage temperature are in a similar range as the intrapersonal variability among different clinical oropharyngeal swab samples.
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Affiliation(s)
- Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Valmik Desai
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
| | - Nela Zavaljevski
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
| | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Xiaoxu Lin
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Ravi Vijaya Satya
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
- Current address: Qiagen Sciences Inc, Frederick, MD 21703, USA
| | - Luis J Martinez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jason M Blaylock
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Current address: Infectious Diseases Service, WRNMMC, Bethesda, MD 20889, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Stephen J Thomas
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Robert A Kuschner
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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Cohen R, Feghali K, Alemayehu S, Komisar J, Hang J, Weina PJ, Coggeshall P, Kamau E, Zapor M. Use of qPCR and genomic sequencing to diagnose Plasmodium ovale wallikeri malaria in a returned soldier in the setting of a negative rapid diagnostic assay. Am J Trop Med Hyg 2013; 89:501-6. [PMID: 23836567 DOI: 10.4269/ajtmh.12-0724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Plasmodium ovale is one of several clinically relevant malaria species known to cause disease in humans. However, in contrast to Plasmodium falciparum and Plasmodium vivax, which are responsible for most cases of human malaria, P. ovale has a wide distribution but low prevalence in tropical regions. Here, we report the case of a soldier returning from Liberia with P. ovale wallikeri malaria. This case highlights the limitations of both microscopy and the malaria rapid diagnostic test for diagnosing infection with P. ovale and for distinguishing P. ovale wallikeri from P. ovale curtisi. To our knowledge, this is the first case report in which quantitative real-time polymerase chain reaction amplification using the Cytochrome B gene, coupled with genomic sequencing of the potra locus, was used for definitive diagnosis of P. ovale wallikeri malaria.
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Affiliation(s)
- Robert Cohen
- Infectious Disease Service, Walter Reed National Military Medical Center, Bethesda, MD, USA.
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Abstract
An unconventional approach for DNA fragmentation was investigated to explore its feasibility as an alternative to the existing DNA fragmentation techniques for next-generation DNA sequencing application. Current methods are based on strong-force liquid shearing or specialized enzymatic treatments. There are shortcomings for these platforms yet to be addressed, including aerosolization of genomic materials, which may result in the cross-contamination and biohazards; the difficulty in multiplexing; and the potential sequence biases. In this proof-of-concept study, we investigated the microwave irradiation as a simple, unbiased, and easy-to-multiplex way to fragment genomic DNA randomly. In addition, heating DNA at high temperature was attempted for the same purpose and for comparison. Adaptive focused acoustic sonication was used as the control. The yield and functionality for the DNA fragments and DNA fragment libraries were analyzed to assess the feasibility and use of the proposed approach. Both microwave irradiation and thermal heating can fragment genomic DNA to the size ranges suitable for next-generation sequencing (NGS) shotgun library preparation. However, both treatments caused severe reduction in PCR amplification efficiency, which led to low production in emulsion PCR (emPCR). The result was improved by amplification prior to emPCR. Further improvements, such as DNA strand repairing, are needed for the method to be applied practically in NGS.
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Affiliation(s)
- Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
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Xiang J, Zang W, Che J, Chen K, Hang J. Regulation network analysis in the esophageal squamous cell carcinoma. Eur Rev Med Pharmacol Sci 2012; 16:2051-2056. [PMID: 23280018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND The incidence of esophageal squamous cell carcinoma (ESCC) has high regional selectivity. The molecular mechanisms of ESCC are complex and involve multiple oncogenes, tumor suppressor genes, receptor tyrosine kinases, cytoplasmic enzymes, and tumor interstitial elements. AIM Here we used bioinformatics to obtain some important genes and pathways involved in ESCC. MATERIALS AND METHODS In this article, we did Affymetrix microarray data collection from three big databases, and then selected all the differentially expressed genes (DEGs) according to some principles. On this basis, we carried out regulation network analysis and pathway enrichment analysis, obtaining ESCC related regulation network analysis, after which we selected significant pathways on regulation network and established TF-pathway regulation network. RESULTS In the transcription factors (TFs) regulation network we found SP1, E2F1, USF2 and SP3 form a local network which suggested that these TFs might play a more important role in ESCC. Some key pathways were also identified, such as P53 signaling pathway, melanoma and prostate cancer pathways. CONCLUSIONS The identification of crucial molecular pathways involved in ESCC would ultimately improve therapeutic effects and facilitate the development of new treatment strategies.
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Affiliation(s)
- J Xiang
- Department of Thoracic Surgery, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Ng S, King CS, Hang J, Clifford R, Lesho EP, Kuschner RA, Cox ED, Stelsel R, Mody R. Severe cavitary pneumonia caused by a non-equi Rhodococcus species in an immunocompetent patient. Respir Care 2012; 58:e47-50. [PMID: 23051922 DOI: 10.4187/respcare.02017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Stephanie Ng
- Department of Internal Medicine, Fort Belvoir Community Hospital, Fort Belvoir, Virginia, USA
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Hang J, Forshey BM, Kochel TJ, Li T, Solórzano VF, Halsey ES, Kuschner RA. Random amplification and pyrosequencing for identification of novel viral genome sequences. J Biomol Tech 2012; 23:4-10. [PMID: 22468136 DOI: 10.7171/jbt.12-2301-001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ssRNA viruses have high levels of genomic divergence, which can lead to difficulty in genomic characterization of new viruses using traditional PCR amplification and sequencing methods. In this study, random reverse transcription, anchored random PCR amplification, and high-throughput pyrosequencing were used to identify orthobunyavirus sequences from total RNA extracted from viral cultures of acute febrile illness specimens. Draft genome sequence for the orthobunyavirus L segment was assembled and sequentially extended using de novo assembly contigs from pyrosequencing reads and orthobunyavirus sequences in GenBank as guidance. Accuracy and continuous coverage were achieved by mapping all reads to the L segment draft sequence. Subsequently, RT-PCR and Sanger sequencing were used to complete the genome sequence. The complete L segment was found to be 6936 bases in length, encoding a 2248-aa putative RNA polymerase. The identified L segment was distinct from previously published South American orthobunyaviruses, sharing 63% and 54% identity at the nucleotide and amino acid level, respectively, with the complete Oropouche virus L segment and 73% and 81% identity at the nucleotide and amino acid level, respectively, with a partial Caraparu virus L segment. The result demonstrated the effectiveness of a sequence-independent amplification and next-generation sequencing approach for obtaining complete viral genomes from total nucleic acid extracts and its use in pathogen discovery.
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Affiliation(s)
- Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA.
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McGann P, Hang J, Clifford RJ, Yang Y, Kwak YI, Kuschner RA, Lesho EP, Waterman PE. Complete sequence of a novel 178-kilobase plasmid carrying bla(NDM-1) in a Providencia stuartii strain isolated in Afghanistan. Antimicrob Agents Chemother 2012; 56:1673-9. [PMID: 22290972 PMCID: PMC3318346 DOI: 10.1128/aac.05604-11] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 01/15/2012] [Indexed: 11/20/2022] Open
Abstract
In response to global concerns over the spread of the New Delhi metallo-β-lactamase gene 1, bla(NDM-1), a monthly surveillance program was initiated in September 2010. All carbapenem-resistant Gram-negative strains forwarded to our facility are screened for this gene. To date, 321 carbapenem-resistant isolates, encompassing 11 bacterial species, have been tested. In February 2011, two strains of Providencia stuartii, submitted from a military hospital in Afghanistan, tested positive for bla(NDM-1). Both strains were identical by pulsed-field gel electrophoresis (PFGE). bla(NDM-1) was carried on a large plasmid, pMR0211, which was sequenced by emulsion PCR and pyrosequencing. pMR0211 is 178,277 bp in size and belongs to incompatibility group A/C. The plasmid consists of a backbone with considerable homology to pAR060302 from Escherichia coli, and it retains many of the antibiotic resistance genes associated with it. The plasmid also shares common elements with the pNDM-HK plasmid, including bla(NDM-1), armA, and sul1. However, gene orientation is reversed, and a 3-kb fragment from this region is absent from pMR0211. pMR0211 also contains additional genes, including the aminoglycoside-modifying enzyme loci aadA and aac(6'), the quinolone resistance gene qnrA, a gene with highest homology to a U32 family peptidase from Shewanella amazonensis, and the bla(OXA-10) gene. The finding of this gene in an intrinsically colistin-resistant species such as Providencia stuartii is especially worrisome, as it renders the organism resistant to nearly every available antibiotic. The presence of multiple insertion sequences and transposons flanking the region containing the bla(NDM-1) gene further highlights the potential mobility associated with this gene.
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Affiliation(s)
- Patrick McGann
- Multidrug Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA.
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Xu W, Hang J, Gao W, Zhao Y, Guo L. Job stress associated with blood pressure among Chinese workers: results from Shiso study. Heart 2011. [DOI: 10.1136/heartjnl-2011-300867.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Hebron HR, Yang Y, Hang J. Purification of genomic DNA with minimal contamination of proteins. J Biomol Tech 2009; 20:278-281. [PMID: 19949702 PMCID: PMC2777350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The purification is based on a set of solutions and a simple centrifugation procedure. Protocols are designed for an easy extraction and purification of genomic DNA from a wide range of samples, including whole blood, buffy coat, bone marrow, body fluids, buccal cells, tissues, mouse tails, etc. RBCs are lysed by dilution into a hypotonic solution. Tissues are broken down and digested by proteinase K in the presence of an anion detergent to release genomic DNA. After precipitation of the detergent and proteins, unique beads that bind proteins, lipids, and RNAs are added to achieve the supreme purity. Genomic DNA is then separated by alcohol precipitation. A proprietary nucleic acid precipitation reagent is used to enhance DNA recovery from low concentration samples. No DNA-binding beads or columns are used in the method, eliminating the problem of low yield and the risk of shearing of genomic DNA. The purified samples are free of proteins, lipids, salts, and RNA contamination. Purified samples are also stable for storage and suitable for all downstream applications.
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Affiliation(s)
| | - Yu Yang
- EdgeBio, Gaithersburg, Maryland 20877, USA
| | - Jun Hang
- EdgeBio, Gaithersburg, Maryland 20877, USA
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Yang Y, Hebron HR, Hang J. A method for preparing DNA sequencing templates using a DNA-binding microplate. J Biomol Tech 2009; 20:165-71. [PMID: 19568455 PMCID: PMC2700467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A DNA-binding matrix was immobilized on the surface of a 96-well microplate and used for plasmid DNA preparation for DNA sequencing. The same DNA-binding plate was used for bacterial growth, cell lysis, DNA purification, and storage. In a single step using one buffer, bacterial cells were lysed by enzymes, and released DNA was captured on the plate simultaneously. After two wash steps, DNA was eluted and stored in the same plate. Inclusion of phosphates in the culture medium was found to enhance the yield of plasmid significantly. Purified DNA samples were used successfully in DNA sequencing with high consistency and reproducibility. Eleven vectors and nine libraries were tested using this method. In 10 microl sequencing reactions using 3 microl sample and 0.25 microl BigDye Terminator v3.1, the results from a 3730xl sequencer gave a success rate of 90-95% and read-lengths of 700 bases or more. The method is fully automatable and convenient for manual operation as well. It enables reproducible, high-throughput, rapid production of DNA with purity and yields sufficient for high-quality DNA sequencing at a substantially reduced cost.
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Affiliation(s)
- Yu Yang
- EdgeBio, Gaithersburg, Maryland, 20877
| | | | - Jun Hang
- EdgeBio, Gaithersburg, Maryland, 20877
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Abstract
The Integrating Waveguide Biosensor was developed for rapid and sensitive detection of bacterial cells, spores, and toxins. A sandwich format of immunoassay was employed using Salmonella as model. The analyte was immunocaptured on the inner surface of the waveguide and then detected by the antibody conjugated with fluorescent dye. The waveguide was illuminated by an excitation light at a 90 degrees angle. The emitted light from fluorescent labels on the surface of the waveguide was efficiently collected and channeled to a detector at the end of the waveguide, while minimizing interference from the excitation light. Utilizing fluorescent dye Cy5, a 635-nm diode laser for excitation, and a photomultiplier tube detector, the Integrating Waveguide Sensor System was able to detect approximately ten captured cells of Salmonella.
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