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Wang C, Yang S, Liu Q, Liu H, Jin S, Zheng J, Xiao X, Hou X, Li J, Ma S, Cui L. Application of Second-Generation Sequencing Technology in Lower Respiratory Tract Infection. J Clin Lab Anal 2024:e25090. [PMID: 39158216 DOI: 10.1002/jcla.25090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/16/2024] [Accepted: 07/29/2024] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND Lower respiratory tract infection (LRTI) has long been an important threat to people's life and health, so the rapid diagnosis of LRTI is of great significance in clinical treatment. In recent years, the development of the sequencing technology provides a new direction for the rapid diagnosis of LRTI. In this review, the advantages and disadvantages of second-generation sequencing techniques represented by metagenomics next-generation sequencing (mNGS) and droplet digital polymerase chain reaction (ddPCR) in LRTI were reviewed. Furthermore, it offers insights into the future trajectory of this technology, highlighting its potential to revolutionise the field of respiratory infection diagnostics. OBJECTIVE This review summarises developments in mechanistic research of second-generation sequencing technology their relationship with clinical practice, providing insights for future research. METHODS Authors conducted a search on PubMed and Web of Science using the professional terms 'Lower respiratory tract infection' and 'droplet digital polymerase chain reaction' and 'metagenomics next generation sequencing'. The obtained literature was then roughly categorised based on their research content. Similar studies were grouped into the same sections, and further searches were conducted based on the keywords of each section. RESULTS Different studies discussed the application of second-generation sequencing technology in LRTI from different angles, including the detection of pathogens of LRTI by mNGS and ddPCR, the prediction ability of drug-resistant bacteria, and comparison with traditional methods. We try to analyse the advantages and disadvantages of the second-generation sequencing technology by combing the research results of mNGS and ddPCR. In addition, the development direction of the second-generation sequencing technology is prospected.
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Affiliation(s)
- Chong Wang
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Shuo Yang
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Qi Liu
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Hongchao Liu
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Shangjia Jin
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Jiajia Zheng
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Xiumei Xiao
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Xin Hou
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Jing Li
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Sisi Ma
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Liyan Cui
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
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Shahrajabian MH, Sun W. The Significance and Importance of dPCR, qPCR, and SYBR Green PCR Kit in the Detection of Numerous Diseases. Curr Pharm Des 2024; 30:169-179. [PMID: 38243947 DOI: 10.2174/0113816128276560231218090436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 01/22/2024]
Abstract
Digital PCR (dPCR) is the latest technique that has become commercially accessible for various types of research. This method uses Taq polymerase in a standard polymerase chain reaction (PCR) to amplify a target DNA fragment from a complex sample, like quantitative PCR (qPCR) and droplet digital PCR (dd- PCR). ddPCR may facilitate microRNA (miRNA) measurement, particularly in liquid biopsy, because it has been proven to be more effective and sensitive, and in this method, ddPCR can provide an unprecedented chance for deoxyribonucleic acid (DNA) methylation research because of its capability to increase sensitivity and precision over conventional PCR-based methods. qPCR has also been found to be a valuable standard technique to measure both copy DNA (cDNA) and genomic DNA (gDNA) levels, although the finding data can be significantly variable and non-reproducible without relevant validation and verification of both primers and samples. The SYBR green quantitative real-time PCR (qPCR) method has been reported as an appropriate technique for quantitative detection and species discrimination, and has been applied profitably in different experiments to determine, quantify, and discriminate species. Although both TaqMan qRT-PCR and SYBR green qRT-PCR are sensitive and rapid, the SYBR green qRT-PCR assay is easy and the TaqMan qRT-PCR assay is specific but expensive due to the probe required. This review aimed to introduce dPCR, qPCR, SYBR green PCR kit, and digital PCR, compare them, and also introduce their advantages in the detection of different diseases.
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Affiliation(s)
- Mohamad Hesam Shahrajabian
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
| | - Wenli Sun
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100086, China
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Delima GK, Ganti K, Holmes KE, Shartouny JR, Lowen AC. Influenza A virus coinfection dynamics are shaped by distinct virus-virus interactions within and between cells. PLoS Pathog 2023; 19:e1010978. [PMID: 36862762 PMCID: PMC10013887 DOI: 10.1371/journal.ppat.1010978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/14/2023] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
When multiple viral populations propagate within the same host environment, they often shape each other's dynamics. These interactions can be positive or negative and can occur at multiple scales, from coinfection of a cell to co-circulation at a global population level. For influenza A viruses (IAVs), the delivery of multiple viral genomes to a cell substantially increases burst size. However, despite its relevance for IAV evolution through reassortment, the implications of this positive density dependence for coinfection between distinct IAVs has not been explored. Furthermore, the extent to which these interactions within the cell shape viral dynamics at the level of the host remains unclear. Here we show that, within cells, diverse coinfecting IAVs strongly augment the replication of a focal strain, irrespective of their homology to the focal strain. Coinfecting viruses with a low intrinsic reliance on multiple infection offer the greatest benefit. Nevertheless, virus-virus interactions at the level of the whole host are antagonistic. This antagonism is recapitulated in cell culture when the coinfecting virus is introduced several hours prior to the focal strain or under conditions conducive to multiple rounds of viral replication. Together, these data suggest that beneficial virus-virus interactions within cells are counterbalanced by competition for susceptible cells during viral propagation through a tissue. The integration of virus-virus interactions across scales is critical in defining the outcomes of viral coinfection.
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Affiliation(s)
- Gabrielle K. Delima
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Katie E. Holmes
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jessica R. Shartouny
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
- * E-mail:
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Shartouny JR, Lee CY, Delima GK, Lowen AC. Beneficial effects of cellular coinfection resolve inefficiency in influenza A virus transcription. PLoS Pathog 2022; 18:e1010865. [PMID: 36121893 PMCID: PMC9521904 DOI: 10.1371/journal.ppat.1010865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/29/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
For diverse viruses, cellular infection with single vs. multiple virions can yield distinct biological outcomes. We previously found that influenza A/guinea fowl/Hong Kong/WF10/99 (H9N2) virus (GFHK99) displays a particularly high reliance on multiple infection in mammalian cells. Here, we sought to uncover the viral processes underlying this phenotype. We found that the need for multiple infection maps to amino acid 26K of the viral PA protein. PA 26K suppresses endonuclease activity and viral transcription, specifically within cells infected at low multiplicity. In the context of the higher functioning PA 26E, inhibition of PA using baloxavir acid augments reliance on multiple infection. Together, these data suggest a model in which sub-optimal activity of the GFHK99 endonuclease results in inefficient priming of viral transcription, an insufficiency which can be overcome with the introduction of additional viral ribonucleoprotein templates to the cell. More broadly, the finding that deficiency in a core viral function is ameliorated through multiple infection suggests that the fitness effects of many viral mutations are likely to be modulated by multiplicity of infection, such that the shape of fitness landscapes varies with viral densities.
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Affiliation(s)
- Jessica R. Shartouny
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
| | - Chung-Young Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
| | - Gabrielle K. Delima
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
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Mendes M, Russell AB. Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes. PLoS Pathog 2021; 17:e1010125. [PMID: 34882752 PMCID: PMC8691639 DOI: 10.1371/journal.ppat.1010125] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/21/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Found in a diverse set of viral populations, defective interfering particles are parasitic variants that are unable to replicate on their own yet rise to relatively high frequencies. Their presence is associated with a loss of population fitness, both through the depletion of key cellular resources and the stimulation of innate immunity. For influenza A virus, these particles contain large internal deletions in the genomic segments which encode components of the heterotrimeric polymerase. Using a library-based approach, we comprehensively profile the growth and replication of defective influenza species, demonstrating that they possess an advantage during genome replication, and that exclusion during population expansion reshapes population composition in a manner consistent with their final, observed, distribution in natural populations. We find that an innate immune response is not linked to the size of a deletion; however, replication of defective segments can enhance their immunostimulatory properties. Overall, our results address several key questions in defective influenza A virus biology, and the methods we have developed to answer those questions may be broadly applied to other defective viruses.
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Affiliation(s)
- Marisa Mendes
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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Amirifar L, Besanjideh M, Nasiri R, Shamloo A, Nasrollahi F, de Barros NR, Davoodi E, Erdem A, Mahmoodi M, Hosseini V, Montazerian H, Jahangiry J, Darabi MA, Haghniaz R, Dokmeci MR, Annabi N, Ahadian S, Khademhosseini A. Droplet-based microfluidics in biomedical applications. Biofabrication 2021; 14. [PMID: 34781274 DOI: 10.1088/1758-5090/ac39a9] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022]
Abstract
Droplet-based microfluidic systems have been employed to manipulate discrete fluid volumes with immiscible phases. Creating the fluid droplets at microscale has led to a paradigm shift in mixing, sorting, encapsulation, sensing, and designing high throughput devices for biomedical applications. Droplet microfluidics has opened many opportunities in microparticle synthesis, molecular detection, diagnostics, drug delivery, and cell biology. In the present review, we first introduce standard methods for droplet generation (i.e., passive and active methods) and discuss the latest examples of emulsification and particle synthesis approaches enabled by microfluidic platforms. Then, the applications of droplet-based microfluidics in different biomedical applications are detailed. Finally, a general overview of the latest trends along with the perspectives and future potentials in the field are provided.
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Affiliation(s)
- Leyla Amirifar
- Mechanical Engineering, Sharif University of Technology, Tehran, Iran, Tehran, 11365-11155, Iran (the Islamic Republic of)
| | - Mohsen Besanjideh
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Tehran, 11365-11155, Iran (the Islamic Republic of)
| | - Rohollah Nasiri
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Tehran, 11365-11155, Iran (the Islamic Republic of)
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Tehran, 11365-11155, Iran (the Islamic Republic of)
| | | | - Natan Roberto de Barros
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Elham Davoodi
- Bioengineering, University of California - Los Angeles, Los Angeles, Los Angeles, 90095, UNITED STATES
| | - Ahmet Erdem
- Bioengineering, University of California - Los Angeles, Los Angeles, Los Angeles, 90095, UNITED STATES
| | | | - Vahid Hosseini
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Hossein Montazerian
- Bioengineering, University of California - Los Angeles, Los Angeles, Los Angeles, 90095, UNITED STATES
| | - Jamileh Jahangiry
- University of California - Los Angeles, Los Angeles, Los Angeles, 90095, UNITED STATES
| | | | - Reihaneh Haghniaz
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Mehmet R Dokmeci
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Nasim Annabi
- Chemical Engineering, UCLA, Los Angeles, Los Angeles, California, 90095, UNITED STATES
| | - Samad Ahadian
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
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Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol 2021; 93:4182-4197. [PMID: 33538349 PMCID: PMC8013307 DOI: 10.1002/jmv.26846] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR) methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.
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Affiliation(s)
- Amir Asri Kojabad
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Research Center for Clinical VirologyTehran University of Medical SciencesTehranIran
| | - Masoumeh Bolandian
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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Piermatteo L, Scutari R, Chirichiello R, Alkhatib M, Malagnino V, Bertoli A, Iapadre N, Ciotti M, Sarmati L, Andreoni M, Ceccherini-Silberstein F, Salpini R, Svicher V. Droplet digital PCR assay as an innovative and promising highly sensitive assay to unveil residual and cryptic HBV replication in peripheral compartment. Methods 2021; 201:74-81. [PMID: 34000391 DOI: 10.1016/j.ymeth.2021.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/29/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Droplet digital PCR is an innovative and promising approach for highly sensitive quantification of nucleic acids that is being increasingly used in the field of clinical virology, including the setting of hepatitis B virus (HBV). Here, we comprehensively report a robust and reproducible ddPCR assay for the highly sensitive quantification of serum HBV-DNA. The assay showed a limit of detection of 4 copies/ml (<1IU/ml) by Probit analysis, showed a good linearity (R2 = 0.94) and a high intra- and inter-run reproducibility with differences between the values obtained in the same run or in two independent runs never exceeding 0.14logcopies/mL and 0.21logcopies/mL, respectively. By analysing serum samples from chronically HBV infected patients (mostly under antiviral treatment), ddPCR successfully quantified serum HBV-DNA in 89.8% of patients with detectable serum HBV-DNA < 20 IU/mL [equivalent to <112copies/ml] by classical Real-Time PCR assay, with a median (IQR) of 8(5-14)IU/mL [45(28-78)copies/ml], and in 66.7% of patients with undetectable serum HBV-DNA, with a median (IQR) of 5(4-9)IU/mL [28(20-50)copies/ml]. Similarly, by analysing serum samples from patients with a serological profile compatible with occult HBV infection (anti-HBc+/HBsAg-), ddPCR successfully quantified serum HBV-DNA in 40% of patients with a median (IQR) value of 1(1-2)IU/mL [5(5-11)copies/ml], in line with the extremely limited viral replication typically observed in occult HBV infection. Overall, the availability of assays for the highly sensitive quantification of serum HBV-DNA can provide an added value in optimizing the diagnosis of occult hepatitis B infection, improving the therapeutic management of chronically HBV infected patients, also in the light of innovative drugs (upcoming in clinical practise) aimed at achieving HBV functional cure.
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Affiliation(s)
- Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Rossana Scutari
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Vincenzo Malagnino
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; Laboratory of Clinical Microbiology and Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Nerio Iapadre
- Infectious Diseases Unit, "San Salvatore Hospital", L' Aquila, Italy
| | - Marco Ciotti
- Laboratory of Clinical Microbiology and Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Loredana Sarmati
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Romina Salpini
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.
| | - Valentina Svicher
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
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Świętoń E, Tarasiuk K, Śmietanka K. Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency. Vet Res 2020; 51:108. [PMID: 32859269 PMCID: PMC7453376 DOI: 10.1186/s13567-020-00833-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/11/2020] [Indexed: 01/11/2023] Open
Abstract
Defective interfering particles (DIPs) of influenza virus are generated through incorporation of highly truncated forms of genome segments, mostly those coding polymerase complex proteins (PB2, PB1, PA). Such particles are able to replicate only in the presence of a virus with the complete genome, thus DIPs may alter the infection outcome by suppressing production of standard virus particles, but also by stimulating the immune response. In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). No clinical signs, mortality or transmission were noted in SPF chickens inoculated with neither virus stock. Turkeys infected with 95/95(DVG-high) showed only slight clinical signs with no mortality, and the virus was transmitted only to birds in direct contact. In contrast, more severe disease, mortality and transmission to direct and indirect contact birds was observed in turkeys infected with 95/95(DVG-low). Apathy, lower water and food intake, respiratory system disorders and a total mortality of 60% were noted. Shedding patterns in contact turkeys indicated more efficient within- and between-host spread of the virus than in 95/95(DVG-high) group. Sequencing of virus genomes showed no mutations that could account for the observed differences in pathogenicity. The results suggest that the abundance of DIPs in the inoculum was the factor responsible for the mild course of infection and disrupted virus transmission.
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Affiliation(s)
- Edyta Świętoń
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Puławy, Poland.
| | - Karolina Tarasiuk
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Puławy, Poland
| | - Krzysztof Śmietanka
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Puławy, Poland
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Collective interactions augment influenza A virus replication in a host-dependent manner. Nat Microbiol 2020; 5:1158-1169. [PMID: 32632248 PMCID: PMC7484227 DOI: 10.1038/s41564-020-0749-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/01/2020] [Indexed: 11/08/2022]
Abstract
Infection with a single influenza A virus (IAV) is only rarely sufficient to initiate productive infection. Instead, multiple viral genomes are often required in a given cell. Here, we show that the reliance of IAV on multiple infection can form an important species barrier. Namely, we find that avian H9N2 viruses representative of those circulating widely at the poultry-human interface exhibit acute dependence on collective interactions in mammalian systems. This need for multiple infection is greatly reduced in the natural host. Quantification of incomplete viral genomes showed that their complementation accounts for the moderate reliance on multiple infection seen in avian cells but not the added reliance seen in mammalian cells. An additional form of virus-virus interaction is needed in mammals. We find that the PA gene segment is a major driver of this phenotype and that both viral replication and transcription are affected. These data indicate that multiple distinct mechanisms underlie the reliance of IAV on multiple infection and underscore the importance of virus-virus interactions in IAV infection, evolution and emergence.
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Poh TY, Ali NABM, Chan LL, Tiew PY, Chotirmall SH. Evaluation of Droplet Digital Polymerase Chain Reaction (ddPCR) for the Absolute Quantification of Aspergillus species in the Human Airway. Int J Mol Sci 2020; 21:E3043. [PMID: 32357408 PMCID: PMC7247686 DOI: 10.3390/ijms21093043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Prior studies illustrate the presence and clinical importance of detecting Aspergillus species in the airways of patients with chronic respiratory disease. Despite this, a low fungal biomass and the presence of PCR inhibitors limits the usefulness of quantitative PCR (qPCR) for accurate absolute quantification of Aspergillus in specimens from the human airway. Droplet digital PCR (ddPCR) however, presents an alternative methodology allowing higher sensitivity and accuracy of such quantification but remains to be evaluated in head-to-head fashion using specimens from the human airway. Here, we implement a standard duplex TaqMan PCR protocol, and assess if ddPCR is superior in quantifying airway Aspergillus when compared to standard qPCR. METHODS The molecular approaches of qPCR and ddPCR were applied to DNA fungal extracts in n = 20 sputum specimens obtained from non-diseased (n = 4), chronic obstructive pulmonary disease (COPD; n = 8) and non-cystic fibrosis bronchiectasis (n = 8) patients where Aspergillus status was known. DNA was extracted and qPCR and ddPCR performed on all specimens with appropriate controls and head-to-head comparisons performed. RESULTS Standard qPCR and ddPCR were both able to detect, even at low abundance, Aspergillus species (Aspergillus fumigatus - A. fumigatus and Aspergillus terreus - A. terreus) from specimens known to contain the respective fungi. Importantly, however, ddPCR was superior for the detection of A. terreus particularly when present at very low abundance and demonstrates greater resistance to PCR inhibition compared to qPCR. CONCLUSION ddPCR has greater sensitivity for A. terreus detection from respiratory specimens, and is more resistant to PCR inhibition, important attributes considering the importance of A. terreus species in chronic respiratory disease states such as bronchiectasis.
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Affiliation(s)
- Tuang Yeow Poh
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore
| | - Nur A’tikah Binte Mohamed Ali
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore
| | - Louisa L.Y. Chan
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore
| | - Pei Yee Tiew
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 169608, Singapore
| | - Sanjay H. Chotirmall
- Translational Respiratory Research Laboratory, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore
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Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR. PLoS One 2019; 14:e0220908. [PMID: 31479459 PMCID: PMC6720028 DOI: 10.1371/journal.pone.0220908] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023] Open
Abstract
Acute respiratory tract infections are a major cause of respiratory morbidity and mortality in pediatric patients worldwide. However, accurate viral and immunologic markers to predict clinical outcomes of this patient population are still lacking. Droplet digital PCR assays for influenza and respiratory syncytial virus (RSV) were designed and performed in 64 respiratory samples from 23 patients with influenza virus infection and 73 samples from 19 patients with RSV infection. Samples of patients with hematologic malignancies, solid tumors, or sickle cell disease were included. Clinical information from institutional medical records was reviewed to assess disease severity. Samples from patients with fever or respiratory symptoms had a significantly higher viral loads than those from asymptomatic patients. Samples from patients with influenza virus and RSV infection collected at presentation had significantly higher viral loads than those collected from patients after completing a course of oseltamivir or ribavirin, respectively. RSV loads correlated positively with clinical symptoms in patients ≤5 years of age, whereas influenza viral loads were associated with clinical symptoms, irrespective of age. Patients receiving antivirals for influenza and RSV had a significant reduction in viral loads after completing therapy. Digital PCR offers an effective method to monitor the efficacy of antiviral treatment for respiratory tract infections in immunocompromised hosts.
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13
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Jacobs NT, Onuoha NO, Antia A, Steel J, Antia R, Lowen AC. Incomplete influenza A virus genomes occur frequently but are readily complemented during localized viral spread. Nat Commun 2019; 10:3526. [PMID: 31387995 PMCID: PMC6684657 DOI: 10.1038/s41467-019-11428-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 07/15/2019] [Indexed: 11/09/2022] Open
Abstract
Segmentation of viral genomes into multiple RNAs creates the potential for replication of incomplete viral genomes (IVGs). Here we use a single-cell approach to quantify influenza A virus IVGs and examine their fitness implications. We find that each segment of influenza A/Panama/2007/99 (H3N2) virus has a 58% probability of being replicated in a cell infected with a single virion. Theoretical methods predict that IVGs carry high costs in a well-mixed system, as 3.6 virions are required for replication of a full genome. Spatial structure is predicted to mitigate these costs, however, and experimental manipulations of spatial structure indicate that local spread facilitates complementation. A virus entirely dependent on co-infection was used to assess relevance of IVGs in vivo. This virus grows robustly in guinea pigs, but is less infectious and does not transmit. Thus, co-infection allows IVGs to contribute to within-host spread, but complete genomes may be critical for transmission.
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Affiliation(s)
- Nathan T Jacobs
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nina O Onuoha
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Alice Antia
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - John Steel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
- Emory-UGA Center of Excellence for Influenza Research and Surveillance, Emory University School of Medicine, Atlanta, GA, USA.
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14
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Martinez-Hernandez F, Garcia-Heredia I, Lluesma Gomez M, Maestre-Carballa L, Martínez Martínez J, Martinez-Garcia M. Droplet Digital PCR for Estimating Absolute Abundances of Widespread Pelagibacter Viruses. Front Microbiol 2019; 10:1226. [PMID: 31244789 PMCID: PMC6581686 DOI: 10.3389/fmicb.2019.01226] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/16/2019] [Indexed: 12/14/2022] Open
Abstract
Absolute abundances of prokaryotes are typically determined by FISH. Due to the lack of a universal conserved gene among all viruses, metagenomic fragment recruitment is commonly used to estimate the relative viral abundance. However, the paucity of absolute virus abundance data hinders our ability to fully understand how viruses drive global microbial populations. The cosmopolitan marine Pelagibacter ubique is host for the highly widespread HTVC010P pelagiphage isolate and the extremely abundant uncultured virus vSAG 37-F6 recently discovered by single-virus genomics. Here we applied droplet digital PCR (ddPCR) to calculate the absolute abundance of these pelagiphage genotypes in the Mediterranean Sea and the Gulf of Maine. Abundances were between 360 and 8,510 virus mL-1 and 1,270–14,400 virus mL-1 for vSAG 37-F6 and HTVC010P, respectively. Illumina PCR-amplicon sequencing corroborated the absence of ddPCR non-specific amplifications for vSAG 37-F6, but showed an overestimation of 6% for HTVC010P from off-targets, genetically unrelated viruses. Absolute abundances of both pelagiphages, two of the most abundance marine viruses, suggest a large viral pelagiphage diversity in marine environments, and show the efficiency and power of ddPCR to disentangle the structure of marine viral communities. Results also highlight the need for a standardized workflow to obtain accurate quantification that allows cross data comparison.
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Affiliation(s)
| | | | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Lucia Maestre-Carballa
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | | | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
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15
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Abstract
Defective viral genomes (DVGs) are generated during viral replication and are unable to carry out a full replication cycle unless coinfected with a full-length virus. DVGs are produced by many viruses, and their presence correlates with alterations in infection outcomes. Historically, DVGs were studied for their ability to interfere with standard virus replication as well as for their association with viral persistence. More recently, a critical role for DVGs in inducing the innate immune response during infection was appreciated. Here we review the role of DVGs of RNA viruses in shaping outcomes of experimental as well as natural infections and explore the mechanisms by which DVGs impact infection outcome.
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Affiliation(s)
- Emmanuelle Genoyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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16
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H5N8 and H7N9 packaging signals constrain HA reassortment with a seasonal H3N2 influenza A virus. Proc Natl Acad Sci U S A 2019; 116:4611-4618. [PMID: 30760600 PMCID: PMC6410869 DOI: 10.1073/pnas.1818494116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Influenza A virus (IAV) has a segmented genome, which (i) allows for exchange of gene segments in coinfected cells, termed reassortment, and (ii) necessitates a selective packaging mechanism to ensure incorporation of a complete set of segments into virus particles. Packaging signals serve as segment identifiers and enable segment-specific packaging. We have previously shown that packaging signals limit reassortment between heterologous IAV strains in a segment-dependent manner. Here, we evaluated the extent to which packaging signals prevent reassortment events that would raise concern for pandemic emergence. Specifically, we tested the compatibility of hemagglutinin (HA) packaging signals from H5N8 and H7N9 avian IAVs with a human seasonal H3N2 IAV. By evaluating reassortment outcomes, we demonstrate that HA segments carrying H5 or H7 packaging signals are significantly disfavored for incorporation into a human H3N2 virus in both cell culture and a guinea pig model. However, incorporation of the heterologous HAs was not excluded fully, and variants with heterologous HA packaging signals were detected at low levels in vivo, including in naïve contact animals. This work indicates that the likelihood of reassortment between human seasonal IAV and avian IAV is reduced by divergence in the RNA packaging signals of the HA segment. These findings offer important insight into the molecular mechanisms governing IAV emergence and inform efforts to estimate the risks posed by H7N9 and H5N8 subtype avian IAVs.
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17
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Seasonal H3N2 and 2009 Pandemic H1N1 Influenza A Viruses Reassort Efficiently but Produce Attenuated Progeny. J Virol 2017. [PMID: 28637755 DOI: 10.1128/jvi.00830-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Reassortment of gene segments between coinfecting influenza A viruses (IAVs) facilitates viral diversification and has a significant epidemiological impact on seasonal and pandemic influenza. Since 1977, human IAVs of H1N1 and H3N2 subtypes have cocirculated with relatively few documented cases of reassortment. We evaluated the potential for viruses of the 2009 pandemic H1N1 (pH1N1) and seasonal H3N2 lineages to reassort under experimental conditions. Results of heterologous coinfections with pH1N1 and H3N2 viruses were compared to those obtained following coinfection with homologous, genetically tagged, pH1N1 viruses as a control. High genotype diversity was observed among progeny of both coinfections; however, diversity was more limited following heterologous coinfection. Pairwise analysis of genotype patterns revealed that homologous reassortment was random while heterologous reassortment was characterized by specific biases. pH1N1/H3N2 reassortant genotypes produced under single-cycle coinfection conditions showed a strong preference for homologous PB2-PA combinations and general preferences for the H3N2 NA, pH1N1 M, and H3N2 PB2 except when paired with the pH1N1 PA or NP. Multicycle coinfection results corroborated these findings and revealed an additional preference for the H3N2 HA. Segment compatibility was further investigated by measuring chimeric polymerase activity and growth of selected reassortants in human tracheobronchial epithelial cells. In guinea pigs inoculated with a mixture of viruses, parental H3N2 viruses dominated but reassortants also infected and transmitted to cage mates. Taken together, our results indicate that strong intrinsic barriers to reassortment between seasonal H3N2 and pH1N1 viruses are few but that the reassortants formed are attenuated relative to parental strains.IMPORTANCE The genome of IAV is relatively simple, comprising eight RNA segments, each of which typically encodes one or two proteins. Each viral protein carries out multiple functions in coordination with other viral components and the machinery of the cell. When two IAVs coinfect a cell, they can exchange genes through reassortment. The resultant progeny viruses often suffer fitness defects due to suboptimal interactions among divergent viral components. The genetic diversity generated through reassortment can facilitate the emergence of novel outbreak strains. Thus, it is important to understand the efficiency of reassortment and the factors that limit its potential. The research described here offers new tools for studying reassortment between two strains of interest and applies those tools to viruses of the 2009 pandemic H1N1 and seasonal H3N2 lineages, which currently cocirculate in humans and therefore have the potential to give rise to novel epidemic strains.
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18
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Heterologous Packaging Signals on Segment 4, but Not Segment 6 or Segment 8, Limit Influenza A Virus Reassortment. J Virol 2017; 91:JVI.00195-17. [PMID: 28331085 DOI: 10.1128/jvi.00195-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/17/2017] [Indexed: 01/07/2023] Open
Abstract
Influenza A virus (IAV) RNA packaging signals serve to direct the incorporation of IAV gene segments into virus particles, and this process is thought to be mediated by segment-segment interactions. These packaging signals are segment and strain specific, and as such, they have the potential to impact reassortment outcomes between different IAV strains. Our study aimed to quantify the impact of packaging signal mismatch on IAV reassortment using the human seasonal influenza A/Panama/2007/99 (H3N2) and pandemic influenza A/Netherlands/602/2009 (H1N1) viruses. Focusing on the three most divergent segments, we constructed pairs of viruses that encoded identical proteins but differed in the packaging signal regions on a single segment. We then evaluated the frequency with which segments carrying homologous versus heterologous packaging signals were incorporated into reassortant progeny viruses. We found that, when segment 4 (HA) of coinfecting parental viruses was modified, there was a significant preference for the segment containing matched packaging signals relative to the background of the virus. This preference was apparent even when the homologous HA constituted a minority of the HA segment population available in the cell for packaging. Conversely, when segment 6 (NA) or segment 8 (NS) carried modified packaging signals, there was no significant preference for homologous packaging signals. These data suggest that movement of NA and NS segments between the human H3N2 and H1N1 lineages is unlikely to be restricted by packaging signal mismatch, while movement of the HA segment would be more constrained. Our results indicate that the importance of packaging signals in IAV reassortment is segment dependent.IMPORTANCE Influenza A viruses (IAVs) can exchange genes through reassortment. This process contributes to both the highly diverse population of IAVs found in nature and the formation of novel epidemic and pandemic IAV strains. Our study sought to determine the extent to which IAV packaging signal divergence impacts reassortment between seasonal IAVs. Our knowledge in this area is lacking, and insight into the factors that influence IAV reassortment will inform and strengthen ongoing public health efforts to anticipate the emergence of new viruses. We found that the packaging signals on the HA segment, but not the NA or NS segments, restricted IAV reassortment. Thus, the packaging signals of the HA segment could be an important factor in determining the likelihood that two IAV strains of public health interest will undergo reassortment.
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