1
|
High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection. Nat Commun 2023; 14:574. [PMID: 36732505 PMCID: PMC9894515 DOI: 10.1038/s41467-022-34256-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/17/2022] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 distribution and circulation dynamics are not well understood due to challenges in assessing genomic data from tissue samples. We develop experimental and computational workflows for high-depth viral sequencing and high-resolution genomic analyses from formalin-fixed, paraffin-embedded tissues and apply them to 120 specimens from six subjects with fatal COVID-19. To varying degrees, viral RNA is present in extrapulmonary tissues from all subjects. The majority of the 180 viral variants identified within subjects are unique to individual tissue samples. We find more high-frequency (>10%) minor variants in subjects with a longer disease course, with one subject harboring ten such variants, exclusively in extrapulmonary tissues. One tissue-specific high-frequency variant was a nonsynonymous mutation in the furin-cleavage site of the spike protein. Our findings suggest adaptation and/or compartmentalized infection, illuminating the basis of extrapulmonary COVID-19 symptoms and potential for viral reservoirs, and have broad utility for investigating human pathogens.
Collapse
|
2
|
Is the ZIKV Congenital Syndrome and Microcephaly Due to Syndemism with Latent Virus Coinfection? Viruses 2021; 13:v13040669. [PMID: 33924398 PMCID: PMC8069280 DOI: 10.3390/v13040669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/02/2021] [Accepted: 04/10/2021] [Indexed: 01/04/2023] Open
Abstract
The emergence of the Zika virus (ZIKV) mirrors its evolutionary nature and, thus, its ability to grow in diversity or complexity (i.e., related to genome, host response, environment changes, tropism, and pathogenicity), leading to it recently joining the circle of closed congenital pathogens. The causal relation of ZIKV to microcephaly is still a much-debated issue. The identification of outbreak foci being in certain endemic urban areas characterized by a high-density population emphasizes that mixed infections might spearhead the recent appearance of a wide range of diseases that were initially attributed to ZIKV. Globally, such coinfections may have both positive and negative effects on viral replication, tropism, host response, and the viral genome. In other words, the possibility of coinfection may necessitate revisiting what is considered to be known regarding the pathogenesis and epidemiology of ZIKV diseases. ZIKV viral coinfections are already being reported with other arboviruses (e.g., chikungunya virus (CHIKV) and dengue virus (DENV)) as well as congenital pathogens (e.g., human immunodeficiency virus (HIV) and cytomegalovirus (HCMV)). However, descriptions of human latent viruses and their impacts on ZIKV disease outcomes in hosts are currently lacking. This review proposes to select some interesting human latent viruses (i.e., herpes simplex virus 2 (HSV-2), Epstein-Barr virus (EBV), human herpesvirus 6 (HHV-6), human parvovirus B19 (B19V), and human papillomavirus (HPV)), whose virological features and co-exposition with ZIKV may provide evidence of the syndemism process, shedding some light on the emergence of the ZIKV-induced global congenital syndrome in South America.
Collapse
|
3
|
Kaur G, Wright K, Verma S, Haynes A, Dufour JM. The Good, the Bad and the Ugly of Testicular Immune Regulation: A Delicate Balance Between Immune Function and Immune Privilege. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1288:21-47. [PMID: 34453730 DOI: 10.1007/978-3-030-77779-1_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The testis is one of several immune privilege sites. These sites are necessary to decrease inflammation and immune responses that could be damaging to the host. For example, inflammation in the brain, eye or placenta could result in loss of cognitive function, vision or rejection of the semi-allogeneic fetus, respectively. In the testis, immune privilege is "good" as it is necessary for protection of the developing auto-immunogenic germ cells. However, there is also a downside or "bad" part of immune privilege, where pathogens and cancers can take advantage of this privilege and persist in the testis as a sanctuary site. Even worse, the "ugly" of privilege is how re-emerging viruses, such as Ebola and Zika viruses, can establish persistence in the testes and be sexually transmitted even months after they have been cleared from the bloodstream. In this review, we will discuss the delicate balance within the testis that provides immune privilege to protect the germ cells while still allowing for immune function to fight off pathogens and tumors.
Collapse
Affiliation(s)
- Gurvinder Kaur
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kandis Wright
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Saguna Verma
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Allan Haynes
- Department of Urology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jannette M Dufour
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| |
Collapse
|
4
|
Kalkeri R, Goebel S, Sharma GD. SARS-CoV-2 Shedding from Asymptomatic Patients: Contribution of Potential Extrapulmonary Tissue Reservoirs. Am J Trop Med Hyg 2020; 103:18-21. [PMID: 32406369 PMCID: PMC7356473 DOI: 10.4269/ajtmh.20-0279] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 05/05/2020] [Indexed: 01/08/2023] Open
Abstract
The ongoing pandemic COVID-19, caused by SARS-CoV-2, has already resulted in more than 3 million cases and more than 200,000 deaths globally. Significant clinical presentations of COVID-19 include respiratory symptoms and pneumonia. In a minority of patients, extrapulmonary organs (central nervous system, eyes, heart, and gut) are affected, with detection of viral RNA in bodily secretions (stool, tears, and saliva). Infection of such extrapulmonary organs may serve as a reservoir for SARS-CoV-2, representing a potential source of viral shedding after the cessation of respiratory symptoms in recovered patients or in asymptomatic individuals. It is extremely important to understand this phenomenon, as individuals with intermittent virus shedding could be falsely identified as reinfected and may benefit from ongoing antiviral treatment. The potential of SARS-CoV-2 infection to rapidly disseminate and infect extrapulmonary organs is likely mediated through the nonstructural and accessory proteins of SARS-CoV-2, which act as ligands for host cells, and through evasion of host immune responses. The focus of this perspective is the extrapulmonary tissues affected by SARS-CoV-2 and the potential implications of their involvement for disease pathogenesis and the development of medical countermeasures.
Collapse
Affiliation(s)
| | | | - Guru Dutt Sharma
- College of Optometry, Western University of Health Sciences, Pomona, California
| |
Collapse
|
5
|
Shim BS, Kwon YC, Ricciardi MJ, Stone M, Otsuka Y, Berri F, Kwal JM, Magnani DM, Jackson CB, Richard AS, Norris P, Busch M, Curry CL, Farzan M, Watkins D, Choe H. Zika Virus-Immune Plasmas from Symptomatic and Asymptomatic Individuals Enhance Zika Pathogenesis in Adult and Pregnant Mice. mBio 2019; 10:e00758-19. [PMID: 31266863 PMCID: PMC6606798 DOI: 10.1128/mbio.00758-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/30/2019] [Indexed: 01/02/2023] Open
Abstract
Preexisting immunity against dengue virus or West Nile virus was previously reported to mediate antibody-dependent enhancement (ADE) of Zika virus (ZIKV) infection in a mouse model. We show here that ZIKV-immune plasma samples from both symptomatic and asymptomatic individuals mediated ZIKV ADE of infection in vitro and in mice. In a lethal infection model with a viral inoculum 10 times higher, both ADE and protection were observed, depending on the amount of infused immune plasma. In a vertical-transmission model, ZIKV-immune plasma infused to timed pregnant mice increased fetal demise and decreased the body weight of surviving fetuses. Depletion of IgG from an immune plasma abolished ADE of infection, and the presence of purified IgG alone mediated ADE of infection. Higher viral loads and proinflammatory cytokines were detected in mice treated with ZIKV-immune plasma samples compared to those receiving control plasma. Together, these data show that passive immunization with homotypic ZIKV antibodies, depending on the concentration, could either worsen or limit a subsequent ZIKV infection.IMPORTANCE Antibody-dependent enhancement (ADE) of virus infection is common to many viruses and is problematic when plasma antibody levels decline to subneutralizing concentrations. ADE of infection is especially important among flaviviruses, many of which are the cause of global health problems. Recently, human plasma samples immune to heterologous flaviviruses were shown to promote Zika virus (ZIKV) infection. Here we showed in immunocompromised mouse models that homologous immune plasma samples protect mice from subsequent infection at high antibody concentrations but that they mediate ADE of infection and increase ZIKV pathogenesis in adult mice and fetal demise during pregnancy at low concentrations.
Collapse
Affiliation(s)
- Byoung-Shik Shim
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Young-Chan Kwon
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Michael J Ricciardi
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Mars Stone
- Viral Reference Laboratory and Repository Core, Blood Systems Research Institute, San Francisco, California, USA
| | - Yuka Otsuka
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Fatma Berri
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Jaclyn M Kwal
- Department of Obstetrics and Gynecology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Diogo M Magnani
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Cody B Jackson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Audrey S Richard
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Philip Norris
- Viral Reference Laboratory and Repository Core, Blood Systems Research Institute, San Francisco, California, USA
- Laboratory Medicine and Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Michael Busch
- Viral Reference Laboratory and Repository Core, Blood Systems Research Institute, San Francisco, California, USA
- Laboratory Medicine and Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Christine L Curry
- Department of Obstetrics and Gynecology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - David Watkins
- Department of Pathology, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| |
Collapse
|
6
|
Shaily S, Upadhya A. Zika virus: Molecular responses and tissue tropism in the mammalian host. Rev Med Virol 2019; 29:e2050. [PMID: 31095819 DOI: 10.1002/rmv.2050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) outbreaks have raised alarm because of reports of congenital Zika virus syndrome in infants. The virus is also known to cause the debilitating Guillain-Barré syndrome in adults. As a result, extensive research has been carried out on the virus over the past few years. To study the molecular responses of viral infectivity in mammals, in vitro two-dimensional and three-dimensional cellular models have been employed. The in vivo models of mouse, pig, chicken, and nonhuman primates are primarily used to investigate the teratogenicity of the virus, to study effects of the virus on specific tissues, and to study the systemic effects of a proposed antiviral agent. The virus exhibits wide tissue tropism in the mammalian host. The major host tissues of viral persistence and propagation are neural tissue, ocular tissue, testicular tissue and placental tissue. An understanding of the function of viral components, viral replication cycle, and the molecular responses elicited in the host tissues is imperative for designing antiviral treatment strategies and for development of vaccines. This review provides an update on ZIKV research models and mammalian host responses with respect to ZIKV tissue infection.
Collapse
Affiliation(s)
- Sangya Shaily
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM'S NMIMS, Mumbai, India
| | - Archana Upadhya
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM'S NMIMS, Mumbai, India
| |
Collapse
|
7
|
Pérez-Padilla J, Paz-Bailey G, Meaney-Delman D, Doyle K, Gary J, Rodriguez DM, Bhatnagar J, Pérez-Rodriguez NM, Montalvo S, Alvarado L, Sharp TM. Persistent Zika Virus Infection Associated with Early Fetal Demise: A Case Report. ACTA ACUST UNITED AC 2019; 9:698-706. [PMID: 31799062 PMCID: PMC6889876 DOI: 10.4236/ojog.2019.95069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background: Infection with Zika virus (ZIKV) during pregnancy is known to cause birth defects and could also be linked to pregnancy loss. Case: A pregnant woman in Puerto Rico contracted ZIKV at 16 weeks gestation. ZIKV RNA persisted in serum from her initial test at 16 weeks through 24 weeks gestation, when fetal demise occurred, and was detected in placental tissue. Conclusion: Prolonged detection of ZIKV RNA in maternal serum was associated with ZIKV RNA detection in the placenta of a patient who experienced fetal demise. While detection of placenta ZIKV RNA does not establish that ZIKV conclusively caused the demise, these findings support emerging evidence that the placenta may serve as a reservoir for ZIKV, which may be associated with prolonged detection of ZIKV RNA in serum.
Collapse
Affiliation(s)
- Janice Pérez-Padilla
- Centers for Disease Control and Prevention (CDC), Dengue Branch, San Juan, Puerto Rico
| | - Gabriela Paz-Bailey
- Centers for Disease Control and Prevention (CDC), Dengue Branch, San Juan, Puerto Rico
| | - Dana Meaney-Delman
- CDC, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, USA
| | - Kate Doyle
- CDC, Division of HIV/AIDS Prevention, Atlanta, GA, USA
| | - Joy Gary
- CDC, Infectious Disease Pathology Branch, Atlanta, GA, USA
| | - Dania M Rodriguez
- Centers for Disease Control and Prevention (CDC), Dengue Branch, San Juan, Puerto Rico
| | - Julu Bhatnagar
- CDC, Infectious Disease Pathology Branch, Atlanta, GA, USA
| | | | - Sara Montalvo
- Ponce Health Sciences University/Saint Luke's Episcopal Hospital, Ponce, Puerto Rico
| | - Luisa Alvarado
- Ponce Health Sciences University/Saint Luke's Episcopal Hospital, Ponce, Puerto Rico
| | - Tyler M Sharp
- Centers for Disease Control and Prevention (CDC), Dengue Branch, San Juan, Puerto Rico
| |
Collapse
|
8
|
Karkhah A, Nouri HR, Javanian M, Koppolu V, Masrour-Roudsari J, Kazemi S, Ebrahimpour S. Zika virus: epidemiology, clinical aspects, diagnosis, and control of infection. Eur J Clin Microbiol Infect Dis 2018; 37:2035-2043. [PMID: 30167886 DOI: 10.1007/s10096-018-3354-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/09/2018] [Indexed: 11/24/2022]
Abstract
Zika virus (ZIKV) is an emerging pathogen of huge public health significance to human beings. Although majority of infections are benign with self-limiting symptoms, the recent outbreak has established an association with the increased incidence of some congenital anomalies such as microcephaly. In other words, due to the large extent of the virus and mosquito vectors, the infection has become a thoughtful health problem for human societies, though now, there are no antiviral therapies or vaccines against this virus. In spite of extensive research carried out by scientists, not so much information has been gathered about this viral infection. In the current review, we prepared an overview of the remarkable progress made in understanding about the epidemiology, immunology, clinical presentation, and diagnosis methods of ZIKV infection.
Collapse
Affiliation(s)
- Ahmad Karkhah
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,Student Research Committee, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Hamid Reza Nouri
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mostafa Javanian
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Veerendra Koppolu
- Scientist Biopharmaceutical Development Medimmune, Gaithersburg, MD, 20878, USA
| | - Jila Masrour-Roudsari
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Sohrab Kazemi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Soheil Ebrahimpour
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
| |
Collapse
|
9
|
da Silva LRC. Zika Virus Trafficking and Interactions in the Human Male Reproductive Tract. Pathogens 2018; 7:E51. [PMID: 29751638 PMCID: PMC6027493 DOI: 10.3390/pathogens7020051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 12/28/2022] Open
Abstract
Sexual transmission of Zika virus (ZIKV) is a matter of great concern. Infectious viral particles can be shed in semen for as long as six months after infection and can be transferred to male and female sexual partners during unprotected sexual intercourse. The virus can be found inside spermatozoa and could be directly transferred to the oocyte during fertilization. Sexual transmission of ZIKV can contribute to the rise in number of infected individuals in endemic areas as well as in countries where the mosquito vector does not thrive. There is also the possibility, as has been demonstrated in mouse models, that the vaginal deposition of ZIKV particles present in semen could lead to congenital syndrome. In this paper, we review the current literature to understand ZIKV trafficking from the bloodstream to the human male reproductive tract and viral interactions with host cells in interstitial spaces, tubule walls, annexed glands and semen. We hope to highlight gaps to be filled by future research and potential routes for vaccine and antiviral development.
Collapse
|