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Kal M, Winiarczyk M, Zarębska-Michaluk D, Odrobina D, Cieśla E, Płatkowska-Adamska B, Biskup M, Pabjan P, Głuszek S, Mackiewicz J. Long-Term Effect of SARS-CoV-2 Infection on the Retinal and Choroidal Microvasculature. J Clin Med 2023; 12:jcm12072528. [PMID: 37048610 PMCID: PMC10095143 DOI: 10.3390/jcm12072528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The purpose of this study was to evaluate the persistent changes in microvascular parameters based on optical coherence tomography angiography (OCTA) in patients hospitalized due to COVID-19 bilateral pneumonia. The case-control prospective study was carried out among 49 patients with COVID-19 and 45 healthy age- and gender-matched 2 and 8 months after hospital discharge. We found a significantly decreased vessel density (VD) in superficial capillary plexus (SCP) in COVID-19 patients. Significantly decreased vessel density (VD) in the superficial capillary plexus (SCP), the deep capillary plexus (DCP), and choriocapillaris (CC), with significantly increased vessel density observed in the choriocapillaris in the foveal area (FCC). The foveal avascular zone in DCP (FAZd) was significantly increased in the COVID-19 group. We found differences between OCTA parameters according to gender. The foveal VD in SCP and DCP was significantly decreased in women compared to men. The FAZ area in SCP (FAZs) and superior VD in the choriocapillaris (SCC) were significantly increased in women. In conclusion, we noticed persistent changes in the ocular parameters of OCTA in COVID-19 patients. At the second follow-up visit, we observed a widened FAZ zone in SCP and decreased VD in some regions of the retina and choroid.
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Said KB, Alsolami A, Alshammari F, Alshammari KF, Alazmi M, Bhardwaj T, Najm MZ, Singh R, Kausar MA. Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach. INFORMATICS IN MEDICINE UNLOCKED 2023; 38:101221. [PMID: 36974160 PMCID: PMC10030443 DOI: 10.1016/j.imu.2023.101221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023] Open
Abstract
The lethal pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has caused the COVID-19 pandemic, posing serious risks to people. The clove-like spike (S) protein that distinguishes coronaviruses from other viruses is important for viral pathogenicity, evolution, and transmission. The investigation of the unique structural mutations of the SARS-CoV-2 spike protein among 34 Asian countries, as well as the resulting phylogenetic relationship, provided critical information in understanding the pathogenesis. This can be utilized for the discovery of possible treatments and vaccine development. The current study analyzed and depicted phylogenetic and evolutionary models useful for understanding SARS-CoV-2 human-human transmission dynamics in Asian regions with shared land borders. Further, integrated bioinformatics analysis was performed to predict the pathogenic potential and stability of 53 mutational positions among 34 coronavirus strains. Mutations at positions N969K, D614G and S884F have deleterious effects on protein function. These findings are crucial because the Asian mutations could potentially provide a vaccine candidate with co-protection against all SARS-CoV-2 strains. This region is vulnerable because of the high population density and the volume of domestic and international travel for business and tourism. These discoveries would also aid in the development of plans for governments and the general populace to implement all required biocontainment protocols common to all countries.
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Affiliation(s)
- Kamaleldin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi Arabia
| | - Ahmed Alsolami
- Department of Internal Medicine, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi Arabia
| | - Fawaz Alshammari
- Department of Dermatology, College of Medicine, University of Ha'il, Ha'il, 55476, Saudi Arabia
| | - Khalid Farhan Alshammari
- Department of Internal Medicine, College of Medicine at University of Ha'il, Ha'il, 2440, Saudi Arabia
| | - Meshari Alazmi
- Department of Information and Computer Science, College of Computer Science and Engineering, University of Ha'il, Ha'il, 81481, Saudi Arabia
| | - Tulika Bhardwaj
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | | | - Rajeev Singh
- Department of Environmental Science, Jamia Millia Islamia (Central University), New Delhi, 110025, India
| | - Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Ha'il, Ha'il, 2440, Saudi Arabia
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Brydak L, Sikora D, Poniedziałek B, Hallmann E, Szymański K, Kondratiuk K, Rzymski P. Association between the Seroprevalence of Antibodies against Seasonal Alphacoronaviruses and SARS-CoV-2 Humoral Immune Response, COVID-19 Severity, and Influenza Vaccination. J Clin Med 2023; 12:jcm12051733. [PMID: 36902520 PMCID: PMC10003754 DOI: 10.3390/jcm12051733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/11/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
The present study assesses the seroprevalence of antibodies against seasonal human alphacoronaviruses 229E and NL63 among adult patients infected with SARS-CoV-2, and its association with the humoral response to SARS-CoV-2 infection and its severity, and influenza vaccination. A serosurvey was conducted to quantify the presence of IgG antibodies against the nucleocapsid of 229E (anti-229E-N) and NL63 (anti-NL63-N), and anti-SARS-CoV-2 IgG antibodies (against nucleocapsid, receptor-binding domain, S2 domain, envelope, and papain-like protease) for 1313 Polish patients. The seroprevalence of anti-229E-N and anti-NL63 in the studied cohort was 3.3% and 2.4%. Seropositive individuals had a higher prevalence of anti-SARS-CoV-2 IgG antibodies, higher titers of the selected anti-SARS-CoV2 antibodies, and higher odds of an asymptomatic SARS-CoV-2 infection (OR = 2.5 for 229E and OR = 2.7 for NL63). Lastly, the individuals vaccinated against influenza in the 2019/2020 epidemic season had lower odds of seropositivity to 229E (OR = 0.38). The 229E and NL63 seroprevalence was below the expected pre-pandemic levels (up to 10%), likely due to social distancing, increased hygiene, and face masking. The study also suggests that exposure to seasonal alphacoronaviruses may improve humoral responses to SARS-CoV-2 while decreasing the clinical significance of its infection. It also adds to accumulating evidence of the favorable indirect effects of influenza vaccination. However, the findings of the present study are of a correlative nature and thereby do not necessarily imply causation.
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Affiliation(s)
- Lidia Brydak
- Department of Influenza Research, National Influenza Center at the National Institute of Public Health NIH—National Research Institute in Warsaw, 00-791 Warsaw, Poland
| | - Dominika Sikora
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 61-701 Poznan, Poland
| | - Barbara Poniedziałek
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznan, Poland
| | - Ewelina Hallmann
- Department of Influenza Research, National Influenza Center at the National Institute of Public Health NIH—National Research Institute in Warsaw, 00-791 Warsaw, Poland
| | - Karol Szymański
- Department of Influenza Research, National Influenza Center at the National Institute of Public Health NIH—National Research Institute in Warsaw, 00-791 Warsaw, Poland
| | - Katarzyna Kondratiuk
- Department of Influenza Research, National Influenza Center at the National Institute of Public Health NIH—National Research Institute in Warsaw, 00-791 Warsaw, Poland
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznań University of Medical Sciences, 60-806 Poznan, Poland
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznan, Poland
- Correspondence:
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The Effect of Reduced Oxygen Saturation on Retinal Microvascularization in COVID-19 Patients with Bilateral Pneumonia Based on Optical Coherence Tomography Study. J Pers Med 2022; 12:jpm12111824. [PMID: 36573721 PMCID: PMC9692346 DOI: 10.3390/jpm12111824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/25/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
The aim of the study was to evaluate changes in the retinal thickness and microvasculature based on optical coherence tomography (OCT) depending on baseline oxygen saturation (SpO2) in patients hospitalized due to COVID-19 bilateral pneumonia. The prospective study was carried out among 62 patients with COVID-19 pneumonia who underwent ophthalmic examination after hospital discharge. They were divided into three groups depending on the oxygen saturation (SpO2) on admission: ≤90% (group 1), >90% and ≤95% (group 2), and >95% (group 3). The following parameters were assessed in the ophthalmological examination and correlated with the baseline SpO2: ganglion cell layer (GCL), the retinal nerve fiber layer (RNFL) in the macular area, RNFL in the peripapillary area, the foveal avascular zone (FAZ) in superficial capillary plexus (SCP) and deep capillary plexus (DCP), vessel density (VD) in SCP, in DCP, and in the choriocapillaris plexus (CC). Baseline saturation ≤90% in COVID-19 patients caused a decrease of VD in some areas of SCP and DCP and an increase in FAZ area in SCP and DCP. In the group of patients with SpO2 ≤ 90% statistically significant thinning of the retina in the inner superior ring (ISR) (p = 0.029), the inner temporal ring (ITR) (p = 0.34), the outer superior ring (OSR) (p = 0.012), and the outer temporal ring (OTR) (p= 0.004)] was observed. The statistically significant thickening of RNFL optic disc and thinning of RNFL retina in some macular areas in patients with SpO2 ≤ 90% were reported. The size of FAZ area in SCP and vessel density were significantly greater in some areas of SCP, DCP, and CC in patients with SpO2 ≤ 90% (p = 0.025). Baseline oxygen saturation ≤90% has been found to influence the ocular parameters of OCT in COVID-19 patients. We noticed a widened FAZ zone in SCP and increased VD in some regions of the retina and choroid as a response to systemic hypoxia.
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Rzymski P, Poniedziałek B, Rosińska J, Rogalska M, Zarębska-Michaluk D, Rorat M, Moniuszko-Malinowska A, Lorenc B, Kozielewicz D, Piekarska A, Sikorska K, Dworzańska A, Bolewska B, Angielski G, Kowalska J, Podlasin R, Oczko-Grzesik B, Mazur W, Szymczak A, Flisiak R. The association of airborne particulate matter and benzo[a]pyrene with the clinical course of COVID-19 in patients hospitalized in Poland. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119469. [PMID: 35580710 PMCID: PMC9106990 DOI: 10.1016/j.envpol.2022.119469] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 05/06/2023]
Abstract
Air pollution can adversely affect the immune response and increase the severity of the viral disease. The present study aimed to explore the relationship between symptomatology, clinical course, and inflammation markers of adult patients with coronavirus disease 2019 (COVID-19) hospitalized in Poland (n = 4432) and air pollution levels, i.e., mean 24 h and max 24 h level of benzo(a)pyrene (B(a)P) and particulate matter <10 μm (PM10) and <2.5 μm (PM2.5) during a week before their hospitalization. Exposures to PM2.5 and B(a)P exceeding the limits were associated with higher odds of early respiratory symptoms of COVID-19 and hyperinflammatory state: interleukin-6 > 100 pg/mL, procalcitonin >0.25 ng/mL, and white blood cells count >11 × 103/mL. Except for the mean 24 h PM10 level, the exceedance of other air pollution parameters was associated with increased odds for oxygen saturation <90%. Exposure to elevated PM2.5 and B(a)P levels increased the odds of oxygen therapy and death. This study evidences that worse air quality is related to increased severity of COVID-19 and worse outcome in hospitalized patients. Mitigating air pollution shall be an integral part of measures undertaken to decrease the disease burden during a pandemic of viral respiratory illness.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806, Poznań, Poland; Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806, Poznań, Poland.
| | - Barbara Poniedziałek
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806, Poznań, Poland.
| | - Joanna Rosińska
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806, Poznań, Poland.
| | - Magdalena Rogalska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-089, Białystok, Poland.
| | | | - Marta Rorat
- Department of Forensic Medicine, Wrocław Medical University, 50-367, Wrocław, Poland; First Infectious Diseases Ward, Gromkowski Regional Specialist Hospital in Wrocław, 51-149, Wrocław, Poland.
| | - Anna Moniuszko-Malinowska
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-089, Białystok, Poland.
| | - Beata Lorenc
- Pomeranian Center of Infectious Diseases, Department of Infectious Diseases, 80-210, Gdańsk, Poland.
| | - Dorota Kozielewicz
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100, Toruń, Poland.
| | - Anna Piekarska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, 90-549, Łódź, Poland.
| | - Katarzyna Sikorska
- Department of Tropical Medicine and Epidemiology, Medical University of Gdańsk, 80-210, Gdańsk, Poland.
| | - Anna Dworzańska
- Department of Infectious Diseases and Hepatology, Medical University of Lublin, 20-059, Lublin, Poland.
| | - Beata Bolewska
- Department of Infectious Diseases, Poznan University of Medical Sciences, 61-701, Poznań, Poland.
| | | | - Justyna Kowalska
- Department of Adults' Infectious Diseases, Medical University of Warsaw, 02-091, Warsaw, Poland.
| | - Regina Podlasin
- Regional Hospital of Infectious Diseases in Warsaw, Warsaw, Poland.
| | - Barbara Oczko-Grzesik
- Department of Infectious Diseases and Hepatology, Medical University of Silesia, 40-055, Katowice, Poland.
| | - Włodzimierz Mazur
- Clinical Department of Infectious Diseases in Chorzów, Medical University of Silesia, Katowice, Poland.
| | - Aleksandra Szymczak
- Department of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Wroclaw Medical University, Wrocław, Poland.
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-089, Białystok, Poland.
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Rzymski P, Poniedziałek B, Rosińska J, Ciechanowski P, Peregrym M, Pokorska-Śpiewak M, Talarek E, Zaleska I, Frańczak-Chmura P, Pilarczyk M, Figlerowicz M, Kucharek I, Flisiak R. Air pollution might affect the clinical course of COVID-19 in pediatric patients. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113651. [PMID: 35594828 PMCID: PMC9110326 DOI: 10.1016/j.ecoenv.2022.113651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/29/2022] [Accepted: 05/12/2022] [Indexed: 05/05/2023]
Abstract
Air pollution, to which children are more susceptible than adults, can promote airway inflammation, potentially exaggerating the effects of respiratory viral infection. This study examined the association between the clinical manifestation of COVID-19 in unvaccinated pediatric patients hospitalized in Poland (n = 766) and levels of particulate matter 2.5 (PM2.5) and benzo(a)pyrene (B(a)P) within a week before hospitalization. Children aged ≤ 12 years exposed to mean and max 24 h B(a)P levels > 1 ng/m3 revealed higher odds of cough, dyspnea, fever, and increased concentrations of inflammatory markers (C-reactive protein, interleukin-6, procalcitonin, white blood cell count). In older patients (13-17 years), elevated mean 24 h B(a)P levels increased odds of dyspnea, fever, and diarrhea, and higher concentrations of C-reactive protein and procalcitonin. Exposure to max 24 h PM2.5 levels > 20 µg/m3 was associated with higher odds of cough, increased concentrations of C-reactive protein (group ≤12 years), and increased procalcitonin concentration (groups ≤12 years and 13-17 years). In both age groups, length of stay was extended in patients exposed to elevated levels of max 24 h PM2.5, mean and max 24 h B(a)P. This study suggests that worse air quality, particularly reflected in increased B(a)P levels, might affect the clinical course of COVID-19 in pediatric patients and adds to the disease burden during a pandemic.
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Affiliation(s)
- Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland; Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznań, Poland.
| | - Barbara Poniedziałek
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland.
| | - Joanna Rosińska
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland.
| | - Przemysław Ciechanowski
- Department of Paediatrics and Infectious Diseases, Regional Hospital in Szczecin, 71-455 Szczecin, Poland.
| | - Michał Peregrym
- Department of Paediatrics and Infectious Diseases, Regional Hospital in Szczecin, 71-455 Szczecin, Poland.
| | - Maria Pokorska-Śpiewak
- Department of Children's Infectious Diseases, Medical University of Warsaw, Regional Hospital of Infectious Diseases in Warsaw, 01-201 Warsaw, Poland.
| | - Ewa Talarek
- Department of Children's Infectious Diseases, Medical University of Warsaw, Regional Hospital of Infectious Diseases in Warsaw, 01-201 Warsaw, Poland.
| | - Izabela Zaleska
- Department of Paediatrics and Infectious Diseases, Wroclaw Medical University, 50-368 Wroclaw, Poland.
| | - Paulina Frańczak-Chmura
- Department of Children's Infectious Diseases, Provincial Jan Boży Hospital in Lublin, 20-089 Lublin, Poland.
| | - Małgorzata Pilarczyk
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, 85-030 Bydgoszcz, Poland.
| | - Magdalena Figlerowicz
- Department of Infectious Diseases and Child Neurology, Poznan University of Medical Sciences, 60-572 Poznan, Poland.
| | - Izabela Kucharek
- 2nd Department of Paediatrics, Centre of Postgraduate Medical Education, Department of Paediatrics and Neonatology with Allergology Center, Central Clinical Hospital of the Ministry of the Interior, 02-507 Warsaw, Poland.
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-089 Białystok, Poland.
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A simulation of geographic distribution for the emergence of consequential SARS-CoV-2 variant lineages. Sci Rep 2022; 12:9999. [PMID: 35705624 PMCID: PMC9199467 DOI: 10.1038/s41598-022-14308-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/06/2022] [Indexed: 11/08/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has been facilitated by the intermittent emergence of consequential variant strains. This study evaluated the geographic disproportionality in the detection of consequential variant lineages across countries. As of November 2021, a total of 40 potentially consequential SARS-CoV-2 variant lineages have been identified. One-hundred repeated simulations that randomly produced consequential variants from overall COVID-19 cases worldwide were performed to evaluate the presence of geographical disproportion in the occurrence of consequential variant outbreaks. Both the total number of reported COVID-19 cases and the number of reported genome sequences in each country showed weak positive correlations with the number of detected consequential lineages in each country. The simulations suggest the presence of geographical disproportion in the occurrence of consequential variant outbreaks. Based on the random occurrence of consequential variants among COVID-19 cases, identified consequential variants occurred more often than expected in the United Kingdom and Africa, whereas they occurred less in other European countries and the Middle East. Simulations of the occurrence of consequential variants by assuming a random occurrence among all COVID-19 cases suggested the presence of biogeographic disproportion. Further studies enrolling unevaluated crucial biogeographical factors are needed to determine the factors underlying the suggested disproportionality.
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8
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Barua A, Grot N, Plawski A. The basis of mink susceptibility to SARS-CoV-2 infection. J Appl Genet 2022; 63:543-555. [PMID: 35396646 PMCID: PMC8993591 DOI: 10.1007/s13353-022-00689-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
Abstract
Of all known airborne diseases in the twenty-first century, coronavirus disease 19 (COVID-19) has the highest infection and death rate. Over the past few decades, animal origin viral diseases, notably those of bats-linked, have increased many folds in humans with cross-species transmissions noted and the ongoing COVID-19 pandemic has emphasized the importance of understanding the evolution of natural hosts in response to viral pathogens. Cross-species transmissions are possible due to the possession of the angiotensin-converting enzyme 2 (ACE2) receptor in animals. ACE2 recognition by SARS-CoV-2 is a critical determinant of the host range, interspecies transmission, and viral pathogenesis. Thus, the phenomenon of breaking the cross-species barrier is mainly associated with mutations in the receptor-binding domain (RBD) of the spike (S) protein that interacts with ACE2. In this review, we raise the issue of cross-species transmission based on sequence alignment of S protein. Based on previous reports and our observations, we can conclude that the occurrence of one of two mutations D614G or Y453F is sufficient for infection of minks by SARS-CoV-2 from humans. Unfortunately, D614G is observed in the world’s most common line of virus B.1.1.7 and the latest SARS-CoV-2 variants B.1.617.1, B.1.617.2, and B.1.617.3 too.
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Affiliation(s)
- Avishak Barua
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-631, Poznań, Poland
| | - Natalia Grot
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Andrzej Plawski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland. .,Department of General and Endocrine Surgery and Gastroenterological Oncology, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznań, Poland.
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9
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Zhang D, Zhu L, Wang Y, Li P, Gao Y. Translational Control of COVID-19 and Its Therapeutic Implication. Front Immunol 2022; 13:857490. [PMID: 35422818 PMCID: PMC9002053 DOI: 10.3389/fimmu.2022.857490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 12/19/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, which has broken out worldwide for more than two years. However, due to limited treatment, new cases of infection are still rising. Therefore, there is an urgent need to understand the basic molecular biology of SARS-CoV-2 to control this virus. SARS-CoV-2 replication and spread depend on the recruitment of host ribosomes to translate viral messenger RNA (mRNA). To ensure the translation of their own mRNAs, the SARS-CoV-2 has developed multiple strategies to globally inhibit the translation of host mRNAs and block the cellular innate immune response. This review provides a comprehensive picture of recent advancements in our understanding of the molecular basis and complexity of SARS-CoV-2 protein translation. Specifically, we summarize how this viral infection inhibits host mRNA translation to better utilize translation elements for translation of its own mRNA. Finally, we discuss the potential of translational components as targets for therapeutic interventions.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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10
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Zhang Y, Jin X, Wang H, Miao Y, Yang X, Jiang W, Yin B. SARS-CoV-2 competes with host mRNAs for efficient translation by maintaining the mutations favorable for translation initiation. J Appl Genet 2022; 63:159-167. [PMID: 34655422 PMCID: PMC8520108 DOI: 10.1007/s13353-021-00665-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/24/2021] [Accepted: 10/03/2021] [Indexed: 11/05/2022]
Abstract
During SARS-CoV-2 proliferation, the translation of viral RNAs is usually the rate-limiting step. Understanding the molecular details of this step is beneficial for uncovering the origin and evolution of SARS-CoV-2 and even for controlling the pandemic. To date, it is unclear how SARS-CoV-2 competes with host mRNAs for ribosome binding and efficient translation. We retrieved the coding sequences of all human genes and SARS-CoV-2 genes. We systematically profiled the GC content and folding energy of each CDS. Considering that some fixed or polymorphic mutations exist in SARS-CoV-2 and human genomes, all algorithms and analyses were applied to both pre-mutate and post-mutate versions. In SARS-CoV-2 but not human, the 5-prime end of CDS had lower GC content and less RNA structure than the 3-prime part, which was favorable for ribosome binding and efficient translation initiation. Globally, the fixed and polymorphic mutations in SARS-CoV-2 had created an even lower GC content at the 5-prime end of CDS. In contrast, no similar patterns were observed for the fixed and polymorphic mutations in human genome. Compared with human RNAs, the SARS-CoV-2 RNAs have less RNA structure in the 5-prime end and thus are more favorable of fast translation initiation. The fixed and polymorphic mutations in SARS-CoV-2 are further amplifying this advantage. This might serve as a strategy for SARS-CoV-2 to adapt to the human host.
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Affiliation(s)
- Yanping Zhang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Xiaojie Jin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Haiyan Wang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Yaoyao Miao
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China.
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11
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Leducq V, Jary A, Bridier-Nahmias A, Daniel L, Zafilaza K, Damond F, Goldstein V, Duval A, Blanquart F, Calvez V, Descamps D, Marcelin AG, Visseaux B. Nosocomial transmission clusters and lineage diversity characterized by SARS-CoV-2 genomes from two large hospitals in Paris, France, in 2020. Sci Rep 2022; 12:1094. [PMID: 35058525 PMCID: PMC8776803 DOI: 10.1038/s41598-022-05085-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
France went through three deadly epidemic waves due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing major public health and socioeconomic issues. We proposed to study the course of the pandemic along 2020 from the outlook of two major Parisian hospitals earliest involved in the fight against COVID-19. Genome sequencing and phylogenetic analysis were performed on samples from patients and health care workers (HCWs) from Bichat (BCB) and Pitié-Salpêtrière (PSL) hospitals. A tree-based phylogenetic clustering method and epidemiological data were used to investigate suspected nosocomial transmission clusters. Clades 20A, 20B and 20C were prevalent during the spring wave and, following summer, clades 20A.EU2 and 20E.EU1 emerged and took over. Phylogenetic clustering identified 57 potential transmission clusters. Epidemiological connections between participants were found for 17 of these, with a higher proportion of HCWs. The joint presence of HCWs and patients suggest viral contaminations between these two groups. We provide an enhanced overview of SARS-CoV-2 phylogenetic changes over 2020 in the Paris area, one of the regions with highest incidence in France. Despite the low genetic diversity displayed by the SARS-CoV-2, we showed that phylogenetic analysis, along with comprehensive epidemiological data, helps to identify and investigate healthcare associated clusters.
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Affiliation(s)
- Valentin Leducq
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, 47-83 Bd de l'hôpital, 75013, Paris, France.
| | - Aude Jary
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, 47-83 Bd de l'hôpital, 75013, Paris, France
| | | | - Lena Daniel
- Université de Paris, Inserm, UMR1137, IAME, Paris, France
| | - Karen Zafilaza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, 47-83 Bd de l'hôpital, 75013, Paris, France
| | - Florence Damond
- Université de Paris, Inserm, UMR1137, IAME, Service de Virologie, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Valérie Goldstein
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière Charles-Foix, Service de Bactériologie Hygiène, Paris, France
| | - Audrey Duval
- Université de Paris, Inserm, UMR1137, IAME, Paris, France
| | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, 47-83 Bd de l'hôpital, 75013, Paris, France
| | - Diane Descamps
- Université de Paris, Inserm, UMR1137, IAME, Service de Virologie, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, 47-83 Bd de l'hôpital, 75013, Paris, France
| | - Benoit Visseaux
- Université de Paris, Inserm, UMR1137, IAME, Service de Virologie, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
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12
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Flisiak R, Rzymski P, Zarębska-Michaluk D, Rogalska M, Rorat M, Czupryna P, Lorenc B, Ciechanowski P, Kozielewicz D, Piekarska A, Pokorska-Śpiewak M, Sikorska K, Tudrujek M, Bolewska B, Angielski G, Kowalska J, Podlasin R, Mazur W, Oczko-Grzesik B, Zaleska I, Szymczak A, Frańczak-Chmura P, Sobolewska-Pilarczyk M, Kłos K, Figlerowicz M, Leszczyński P, Kucharek I, Grabowski H. Demographic and Clinical Overview of Hospitalized COVID-19 Patients during the First 17 Months of the Pandemic in Poland. J Clin Med 2021; 11:jcm11010117. [PMID: 35011858 PMCID: PMC8745464 DOI: 10.3390/jcm11010117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Long-term analyses of demographical and clinical characteristics of COVID-19 patients can provide a better overview of the clinical course of the disease. They can also help understand whether changes in infection symptomatology, disease severity, and outcome occur over time. We aimed to analyze the demographics, early symptoms of infection, laboratory parameters, and clinical manifestation of COVID-19 patients hospitalized during the first 17 months of the pandemic in Poland (March 2020-June 2021). The patients' demographical and clinical data (n = 5199) were extracted from the national SARSTer database encompassing 30 medical centers in Poland and statistically assessed. Patients aged 50-64 were most commonly hospitalized due to COVID-19 regardless of the pandemic period. There was no shift in the age of admitted patients and patients who died throughout the studied period. Men had higher C-reactive protein and interleukin-6 levels and required oxygenation and mechanical ventilation more often. No gender difference in fatality rate was seen, although the age of males who died was significantly lower. A share of patients with baseline SpO2 < 91%, presenting respiratory, systemic and gastrointestinal symptoms was higher in the later phase of a pandemic than in the first three months. Cough, dyspnea and fever were more often presented in men, while women had a higher frequency of anosmia, diarrhea, nausea and vomiting. This study shows some shifts in SARS-CoV-2 pathogenicity between March 2020 and July 2021 in the Polish cohort of hospitalized patients and documents various gender-differences in this regard. The results represent a reference point for further analyses conducted under the dominance of different SARS-CoV-2 variants.
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Affiliation(s)
- Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-089 Bialystok, Poland;
- Correspondence: (R.F.); (P.R.); (D.Z.-M.)
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznan, Poland
- Correspondence: (R.F.); (P.R.); (D.Z.-M.)
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases, Jan Kochanowski University, 25-369 Kielce, Poland
- Correspondence: (R.F.); (P.R.); (D.Z.-M.)
| | - Magdalena Rogalska
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-089 Bialystok, Poland;
| | - Marta Rorat
- Department of Forensic Medicine, Wrocław Medical University, 50-367 Wroclaw, Poland;
- First Infectious Diseases Ward, Gromkowski Regional Specialist Hospital in Wrocław, 51-149 Wroclaw, Poland
| | - Piotr Czupryna
- Department of Infectious Diseases and Neuroinfections, Medical University of Białystok, 15-089 Bialystok, Poland;
| | - Beata Lorenc
- Pomeranian Center of Infectious Diseases, Department of Infectious Diseases, 80-210 Gdansk, Poland;
| | - Przemysław Ciechanowski
- Department of Paediatrics and Infectious Diseases, Regional Hospital in Szczecin, 71-455 Szczecin, Poland;
| | - Dorota Kozielewicz
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland; (D.K.); (M.S.-P.)
| | - Anna Piekarska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, 90-549 Lodz, Poland;
| | - Maria Pokorska-Śpiewak
- Department of Children’s Infectious Diseases, Medical University of Warsaw, 01-201 Warsaw, Poland;
| | - Katarzyna Sikorska
- Department of Tropical Medicine and Epidemiology, Medical University of Gdańsk, 80-210 Gdansk, Poland;
| | - Magdalena Tudrujek
- Department of Infectious Diseases and Hepatology, Medical University of Lublin, 20-059 Lublin, Poland;
| | - Beata Bolewska
- Department of Infectious Diseases, Poznan University of Medical Sciences, 61-701 Poznan, Poland;
| | | | - Justyna Kowalska
- Department of Adults’ Infectious Diseases, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Regina Podlasin
- Regional Hospital of Infectious Diseases in Warsaw, 01-301 Warsaw, Poland;
| | - Włodzimierz Mazur
- Clinical Department of Infectious Diseases in Chorzów, Medical University of Silesia, 41-500 Katowice, Poland;
| | - Barbara Oczko-Grzesik
- Department of Infectious Diseases and Hepatology, Medical University of Silesia, 40-055 Katowice, Poland;
| | - Izabela Zaleska
- Department of Paediatrics and Infectious Diseases, Wroclaw Medical University, 50-367 Wroclaw, Poland;
| | - Aleksandra Szymczak
- Department of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Wroclaw Medical University, 51-149 Wrocław, Poland;
| | - Paulina Frańczak-Chmura
- Department of Children’s Infectious Diseases, Provincial Jan Boży Hospital, 20-089 Lublin, Poland;
| | - Małgorzata Sobolewska-Pilarczyk
- Department of Infectious Diseases and Hepatology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland; (D.K.); (M.S.-P.)
| | - Krzysztof Kłos
- Department of Infectious Diseases and Allergology, Military Institute of Medicine, 04-141 Warsaw, Poland;
| | - Magdalena Figlerowicz
- Department of Infectious Diseases and Child Neurology, Poznan University of Medical Sciences, 60-572 Poznan, Poland;
| | - Piotr Leszczyński
- Department of Rheumatology, Rehabilitation and Internal Medicine, Poznan University of Medical Sciences, 61-701 Poznan, Poland;
| | - Izabela Kucharek
- 2nd Department of Paediatrics, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland;
| | - Hubert Grabowski
- General, Endocrine and Transplant Surgery Department, Medical University of Gdańsk, 80-214 Gdansk, Poland;
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13
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Xi H, Jiang H, Juhas M, Zhang Y. Multiplex Biosensing for Simultaneous Detection of Mutations in SARS-CoV-2. ACS OMEGA 2021; 6:25846-25859. [PMID: 34632242 PMCID: PMC8491437 DOI: 10.1021/acsomega.1c04024] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/10/2021] [Indexed: 05/02/2023]
Abstract
COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has become the world's largest public health emergency of the past few decades. Thousands of mutations were identified in the SARS-CoV-2 genome. Some mutants are more infectious and may replace the original strains. Recently, B.1.1.7(Alpha), B1.351(Beta), and B.1.617.2(Delta) strains, which appear to have increased transmissibility, were detected. These strains accounting for the high proportion of newly diagnosed cases spread rapidly over the world. Particularly, the Delta variant has been reported to account for a vast majority of the infections in several countries over the last few weeks. The application of biosensors in the detection of SARS-CoV-2 is important for the control of the COVID-19 pandemic. Due to high demand for SARS-CoV-2 genotyping, it is urgent to develop reliable and efficient systems based on integrated multiple biosensor technology for rapid detection of multiple SARS-CoV-2 mutations simultaneously. This is important not only for the detection and analysis of the current but also for future mutations. Novel biosensors combined with other technologies can be used for the reliable and effective detection of SARS-CoV-2 mutants.
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Affiliation(s)
- Hui Xi
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
| | - Hanlin Jiang
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
| | - Mario Juhas
- Medical
and Molecular Microbiology Unit, Department of Medicine, Faculty of
Science and Medicine, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Yang Zhang
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
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14
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Miljanovic D, Milicevic O, Loncar A, Abazovic D, Despot D, Banko A. The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe. Front Microbiol 2021; 12:691154. [PMID: 34220784 PMCID: PMC8250835 DOI: 10.3389/fmicb.2021.691154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/19/2021] [Indexed: 12/23/2022] Open
Abstract
March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations.
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Affiliation(s)
- Danijela Miljanovic
- Virology Laboratory, Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, Belgrade, Serbia
| | - Ognjen Milicevic
- Faculty of Medicine, Institute for Medical Statistics and Informatics, University of Belgrade, Belgrade, Serbia
| | - Ana Loncar
- Laboratory of Molecular Microbiology, Institute for Biocides and Medical Ecology, Belgrade, Serbia
| | - Dzihan Abazovic
- Biocell Hospital, Belgrade, Serbia
- Emergency Medical Centre of Montenegro, Podgorica, Montenegro
| | - Dragana Despot
- Laboratory of Molecular Microbiology, Institute for Biocides and Medical Ecology, Belgrade, Serbia
| | - Ana Banko
- Virology Laboratory, Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, Belgrade, Serbia
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