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Kakuk B, Tombácz D, Balázs Z, Moldován N, Csabai Z, Torma G, Megyeri K, Snyder M, Boldogkői Z. Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome. Sci Rep 2021; 11:14487. [PMID: 34262076 PMCID: PMC8280142 DOI: 10.1038/s41598-021-93593-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/28/2021] [Indexed: 02/08/2023] Open
Abstract
Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice variants. In this work, we profile the human cytomegalovirus transcriptome using two third-generation LRS platforms: the Sequel from Pacific BioSciences, and MinION from Oxford Nanopore Technologies. We carried out both cDNA and direct RNA sequencing, and applied the LoRTIA software, developed in our laboratory, for the transcript annotations. This study identified a large number of novel transcript variants, including splice isoforms and transcript start and end site isoforms, as well as putative mRNAs with truncated in-frame ORFs (located within the larger ORFs of the canonical mRNAs), which potentially encode N-terminally truncated polypeptides. Our work also disclosed a highly complex meshwork of transcriptional read-throughs and overlaps.
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Affiliation(s)
- Balázs Kakuk
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
- MTA-SZTE Momentum GeMiNI Research Group, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr, Stanford, CA, USA
| | - Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary
| | - Klára Megyeri
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr, Stanford, CA, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, 6720, Szeged, Hungary.
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Cytomegalovirus infection in pregnancy - An update. Eur J Obstet Gynecol Reprod Biol 2020; 258:216-222. [PMID: 33454510 DOI: 10.1016/j.ejogrb.2020.12.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022]
Abstract
Cytomegalovirus (CMV) is a ubiquitous DNA virus with a global seroprevalence of 83 %. It is the most common pathogen causing teratogenic congenital infection. It is therefore a major public health concern. Maternal infection is associated with congenital CMV (cCMV), the leading cause of non-genetic sensorineural hearing loss. cCMV also causes impairment of cognitive development and cerebral palsy. Transmission of CMV occurs through direct contact with bodily fluids such as saliva, urine or semen from someone who is actively shedding the virus. Transmission rates are higher after primary infection with the rate of transmission increasing with gestational age. Severe fetal effects are however more common when infection occurs before 20weeks. Past infection does not confer immunity to mother or protect the fetus. cCMV may present with cerebral or extracerebral abnormalities on ultrasound, fetal growth restriction and fetal loss. Diagnosis of primary maternal CMV in pregnancy should be based on seroconversion in pregnancy (de novo appearance of virus-specific immunoglobulin G (IgG) in the serum of pregnant women who were previously seronegative) or on detection of specific immunoglobulin M (IgM) and IgG antibodies in association with low IgG avidity. Prenatal diagnosis of fetal CMV is imperfect and based on amniocentesis performed at least 8 weeks after presumed maternal infection and after 17 weeks of gestation. Hygiene information and education of pregnant women is currently the most effective strategy for prevention of CMV infection. The role of vaccines, antiviral drugs and immunoglobulins remains unproven.
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Balázs Z, Tombácz D, Szűcs A, Snyder M, Boldogkői Z. Dual Platform Long-Read RNA-Sequencing Dataset of the Human Cytomegalovirus Lytic Transcriptome. Front Genet 2018; 9:432. [PMID: 30319694 PMCID: PMC6170618 DOI: 10.3389/fgene.2018.00432] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/11/2018] [Indexed: 02/03/2023] Open
Affiliation(s)
- Zsolt Balázs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, United States
| | - Attila Szűcs
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, United States
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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Shi TL, Huang LJ, Xiong YQ, Zhong YY, Yang JJ, Fu T, Lei XF, Chen Q. The risk of herpes simplex virus and human cytomegalovirus infection during pregnancy upon adverse pregnancy outcomes: A meta-analysis. J Clin Virol 2018; 104:48-55. [DOI: 10.1016/j.jcv.2018.04.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/13/2018] [Accepted: 04/24/2018] [Indexed: 12/12/2022]
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Cheng N, Wang D, Zhou Z, Cheng Z, Dong L, Zhang R, Zhang Y, Zheng T, Bai Y. Interaction between HCMV infection and PAX9 gene polymorphisms in low birth weight infants. J Matern Fetal Neonatal Med 2015; 29:2040-3. [DOI: 10.3109/14767058.2015.1073253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Yan XC, Wang JH, Wang B, Huang LL, Zhou LQ, Zhu B, Liang Y. Study of human cytomegalovirus replication in body fluids, placental infection, and miscarriage during the first trimester of pregnancy. J Med Virol 2015; 87:1046-53. [PMID: 25732959 DOI: 10.1002/jmv.24158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2015] [Indexed: 11/08/2022]
Abstract
Intrauterine infection caused by human cytomegalovirus (HCMV) can lead to embryo, fetal, and neonatal damage. The prevalence of HCMV replication in body fluids (blood, urine, and cervicovaginal secretion) was investigated, and its effects on HCMV vertical transmission and miscarriages in early pregnant women were evaluated. HCMV DNA in body fluids was detected in 1,064 early pregnant women (624 normal pregnancies and 440 miscarriages). There were 101 cases who were HCMV DNA positive in cervicovaginal secretion and the rates were 10.9% (48/440 cases) and 8.5% (53/624 cases) in miscarriages and normal pregnancies, respectively (P > 0.05). A total of 101 cases (63 and 38 cases with and without HCMV DNA in cervicovaginal secretion, respectively) were given HCMV DNA detection in placental villi/deciduas. There were five cases (7.9%; two normal pregnancies and three miscarriages) with HCMV DNA in placental villi/deciduas among the 63 cases with HCMV DNA in cervicovaginal secretion, whereas none of the other 38 cases were detected HCMV DNA positive in their placental villi/deciduas. The percentage of HCMV DNA in placental villi/deciduas was higher in miscarriage group (9.1% [3/33]) than that in the normal pregnancy group (6.7% [2/30]), but there was no statistical significance (P > 0.05). Two cases with a higher HCMV loads in cervicovaginal secretion and placental villi/deciduas had miscarriages. These findings suggest that HCMV replication in cervicovaginal secretion can involve in placental HCMV infection, and high HCMV DNA loads in cervicovaginal secretion and placental villi/deciduas are associated with miscarriage.
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Affiliation(s)
- Xiao Chuan Yan
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Syridou G, Skevaki C, Kafetzis DA. Intrauterine infection with parvovirus B19 and CMV: implications in early and late gestation fetal demise. Expert Rev Anti Infect Ther 2014; 3:651-61. [PMID: 16107203 DOI: 10.1586/14787210.3.4.651] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In utero viral infections have been associated with an adverse pregnancy outcome and may have a causative role in the unexplained fetal death file. Parvovirus B19 and cytomegalovirus are among the most common pathogens implicated in fetal loss cases. Parvovirus B19 has been reported to account for cases of spontaneous abortions, intrauterine fetal death and nonimmune hydrops fetalis, whereas cytomegalovirus accounts for nonimmune hydrops fetalis, intrauterine growth retardation and congenital anomalies. This review aims to summarize the current literature in an attempt to underline the need for routine screening, close follow-up and prevention. A better understanding of the pathogenetic mechanisms of viral infections during the crucial time of organogenesis, along with early detection, may contribute to the reduction in stillbirth rate.
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Affiliation(s)
- Garyfallia Syridou
- Second Department of Pediatrics, P and A Kiriakou Children's Hospital, University of Athens, Thevon & Livadias Str, GR-11527, Athens, Greece.
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Long-term impact of intrauterine MCMV infection on development of offspring nervous system. ACTA ACUST UNITED AC 2011; 31:371. [DOI: 10.1007/s11596-011-0383-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Indexed: 10/18/2022]
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Juanjuan C, Yan F, Li C, Haizhi L, Ling W, Xinrong W, Juan X, Tao L, Zongzhi Y, Suhua C. Murine model for congenital CMV infection and hearing impairment. Virol J 2011; 8:70. [PMID: 21320351 PMCID: PMC3045346 DOI: 10.1186/1743-422x-8-70] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 02/15/2011] [Indexed: 11/28/2022] Open
Abstract
Background Congenital cytomegalovirus (CMV) infection is the leading cause of sensorineural hearing loss (SNHL), and SNHL is the most frequent sequela of congenital CMV infection. But the pathogenic mechanism remains unknown, and there is no ideal CMV intrauterine infection animal model to study the mechanisms by which SNHL develops. Methods We established the congenital murine cytomegalovirus (MCMV) infection model by directly injecting the virus into the placenta on day 12.5 of gestation. Then, we observed the development and the MCMV congenital infection rate of the fetuses on the day they were born. Furthermore, we detected the auditory functions, the conditions of the MCMV infection, and the histological change of the inner ears of 28-day-old and 70-day-old offspring. Results Both the fetal loss rate and the teratism rate of offspring whose placentas were inoculated with MCMV increased, and their body length, head circumference, and weight decreased. The hearing level of offspring both decreased at both 28- and 70-days post birth; the 70-day-old mice developed lower hearing levels than did the 28-day old mice. No significant inflammatory changes in the cochleae of the mice were observed. MCMV DNA signals were mainly detected in the spiral ganglion neurons and the endolymph area, but not in the perilymph area. The number of neurons decreased, and their ultrastructures changed. Moreover, with age, the number of neurons dramatically decreased, and the ultrastructural lesions of neurons became much more severe. Conclusions The results suggest that the direct injection of MCMV into the placenta may efficiently cause fetal infection and disturb the intrauterine development of the fetus, and placental inoculation itself has no obvious adverse effects on offspring. The reduction in the number of spiral ganglion neurons and the ultrastructural lesions of the neurons may be the major cause of congenital CMV infection-induced progressive SNHL.
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Affiliation(s)
- Chen Juanjuan
- Department of Obstetrics and Gynecology, Affiliated Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
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Heimonen A, Janket SJ, Meurman JH, Furuholm J, Ackerson LK, Kaaja R. Oral health care patterns and the history of miscarriage. Oral Dis 2009; 14:734-40. [PMID: 19193203 DOI: 10.1111/j.1601-0825.2008.01460.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Oral infections can trigger the production of pro-inflammatory mediators that may be risk factors for miscarriage. We investigated whether oral health care patterns that may promote or alleviate oral inflammation were associated with the history of miscarriage in 328 all-Caucasian women. MATERIALS AND METHODS Of 328 women in this cross-sectional cohort, 74 had history of miscarriage (HMC). Medical, dental and sociodemographic data were collected through clinical examinations, medical record searches and structured questionnaires. RESULTS The multivariate regression analyses indicated that urgency-based dental treatment demonstrated a significant association [odds ratio (OR) = 2.54; 95% confidence interval (CI): 1.21-5.37; P = 0.01] and preventive dental treatment demonstrated a marginally significant inverse association (OR = 0.53; CI: 0.26-1.06; P = 0.07) with HMC. Self-rated poor oral health had a non-significant positive association with HMC (OR 1.60; CI: 0.88-2.90). CONCLUSION Our results provide sufficient evidence for hypothesis generation to test whether other precise measures of oral inflammation are associated with adverse birth outcomes.
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Affiliation(s)
- A Heimonen
- Institute of Dentistry, Oulu University and Hospital, Oulu, Finland.
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Liu Z, Tian Y, Wang B, Yan Z, Qian D, Ding S, Song X, Bai Z, Li L. Serum proteomics with SELDI-TOF-MS in congenital human cytomegalovirus hepatitis. J Med Virol 2007; 79:1500-5. [PMID: 17705191 DOI: 10.1002/jmv.20927] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Human cytomegalovirus (HCMV) is a widespread pathogen, the most common congenital viral infection, and the leading cause of infant hepatitis syndrome. In this study, serum samples were collected from 20 HCMV-infected infants with hepatitis and 25 controls. Of the 25 infants in the control group, 5 were infected with HCMV but without hepatitis, 10 had hepatitis but no HCMV infection, and 10 were healthy. Proteomic expression in the serum was detected by WCX2 chips and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS), to identify serum protein biomarkers in infants with hepatitis syndrome resulting from HCMV. Fifteen protein peaks were distinctly different among the four groups in the mass range from 2,000 to 20,000 Da. Of these 15 peaks, 4 at 4,349.8, 5,808.7, 7,935.6, and 8,885.9 Da were significantly different between the congenital HCMV-infected infants with hepatitis and the controls. Five peaks were distinctly up-regulated in the infants with HCMV infection (3,266.8, 5,638.5, 5,909.1, 7,771.4, and 15,835.6 Da) compared to those without HCMV infection. Two proteins at 4,600.1 and 5,704.3 were up-regulated in infants with HMCV infection but no hepatitis. Four protein peaks were markedly different (7,567.0, 13,744.8, 15,100.7, and 15,915.0 Da) between the infants with hepatitis and the other controls. Comparison of the differentially expressed proteins' properties with those available on an international database suggest that specific serum proteins such as the augmenter of liver regeneration, pre-albumin, and haptoglobin closely related to liver function, and cytokines such as beta-defensins 31 and 8, and macrophage-derived chemokine, among others, are involved in HMCV infection and the pathogenesis of HMCV-induced hepatitis in infants.
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MESH Headings
- Blood Proteins/analysis
- Blood Proteins/chemistry
- Chemokines/biosynthesis
- Chemokines/blood
- Cytochrome Reductases/blood
- Cytomegalovirus Infections/blood
- Cytomegalovirus Infections/complications
- Cytomegalovirus Infections/congenital
- Haptoglobins/analysis
- Hepatitis, Viral, Human/blood
- Hepatitis, Viral, Human/congenital
- Hepatitis, Viral, Human/etiology
- Hepatitis, Viral, Human/physiopathology
- Humans
- Infant
- Macrophages/immunology
- Macrophages/metabolism
- Molecular Weight
- Oxidoreductases Acting on Sulfur Group Donors
- Proteomics
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- beta-Defensins/blood
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Affiliation(s)
- Zhijun Liu
- Department of Microbiology, Key Laboratory of Medicine and Biotechnology of Qingdao, Qingdao University Medical College, Qingdao, Shandong, China
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Munro SC, Trincado D, Hall B, Rawlinson WD. Symptomatic infant characteristics of congenital cytomegalovirus disease in Australia. J Paediatr Child Health 2005; 41:449-52. [PMID: 16101982 DOI: 10.1111/j.1440-1754.2005.00665.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Human cytomegalovirus (CMV) is the most common cause of viral intrauterine infection. In utero transmission can occur during primary maternal infection, reactivation or reinfection of seropositive mothers. OBJECTIVE To describe the aetiology and clinical features of infants diagnosed with congenital CMV and to document maternal factors that were presented. METHODS Active national surveillance was initiated in 1999 in collaboration with the Australian Paediatric Surveillance Unit. RESULTS Monthly notifications resulted in 70 cases of congenital CMV being identified between 1999 and 2003. Nearly all of the cases were symptomatic with the most common clinical sequelae reported in infected infants being jaundice, thrombocytopaenia, hepatomegaly, petechiae, purpura and splenomegaly. Almost half (43.5%) of the infants had central nervous system (CNS) complications, such as microcephaly, chorioretinitis, sensorineural hearing loss, intracranial calcifications, developmental delay or seizures, with over half presenting two or more CNS abnormalities. Maternal febrile illness was noted in 54.8% of the cases. The majority of mothers were primiparous (46.4%) or secundiparous (39.3%), indicating two different population groups at risk of primary CMV infection. CONCLUSION This study documents symptomatic congenital CMV cases in Australia.
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Affiliation(s)
- Sian C Munro
- Virology Division, Department of Microbiology, SEALS, Prince of Wales Hospital, New South Wales, Australia.
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Abstract
The polymerase chain reaction (PCR) is a powerful molecular biologic technique that permits detection and identification of infinitesimal quantities of DNA. It is well suited to the diagnosis of infectious posterior segment ocular inflammatory disease. In this review, the basic biochemistry of PCR, indications for its use, strengths and limitations to the technique, and examples of clinical application of PCR to posterior segment disease will be discussed. Emerging uses of PCR in linking pathogen to disease will also be outlined. After completion of this article, the reader will be able to describe the basic biochemistry and practical application of PCR in the diagnosis of posterior segment inflammatory disease, list the indications, advantages, and disadvantages of the technique, and outline the application of PCR diagnostics to individual differential diagnoses.
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Affiliation(s)
- Russell N Van Gelder
- Department of Ophthalmology and Visual Sciences, Department of Molecular Biology and Pharmacology, Washington University Medical School, Campus Box 8096, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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