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Hijano DR, Ferrolino JA, Gu Z, Brazelton JN, Zhu H, Suganda S, Glasgow HL, Dallas RH, Allison KJ, Maron G, Darji H, Tang L, Fabrizio TP, Webby RJ, Hayden RT. Digital PCR to Measure SARS-CoV-2 RNA, Variants, and Outcomes in Youth. J Pediatric Infect Dis Soc 2023; 12:618-626. [PMID: 37956414 PMCID: PMC10725239 DOI: 10.1093/jpids/piad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND The role of SARS-CoV-2 viral load in predicting contagiousness, disease severity, transmissibility, and clinical decision-making continues to be an area of great interest. However, most studies have been in adults and have evaluated SARS-CoV-2 loads using cycle thresholds (Ct) values, which are not standardized preventing consistent interpretation critical to understanding clinical impact and utility. Here, a quantitative SARS-CoV-2 reverse-transcription digital PCR (RT-dPCR) assay normalized to WHO International Units was applied to children at risk of severe disease diagnosed with COVID-19 at St. Jude Children's Research Hospital between March 28, 2020, and January 31, 2022. METHODS Demographic and clinical information from children, adolescents, and young adults treated at St. Jude Children's Research Hospital were abstracted from medical records. Respiratory samples underwent SARS-CoV-2 RNA quantitation by RT-dPCR targeting N1 and N2 genes, with sequencing to determine the genetic lineage of infecting virus. RESULTS Four hundred and sixty-two patients aged 0-24 years (median 11 years old) were included during the study period. Most patients were infected by the omicron variant (43.72%), followed by ancestral strain (22.29%), delta (13.20%), and alpha (2.16%). Viral load at presentation ranged from 2.49 to 9.14 log10 IU/mL, and higher viral RNA loads were associated with symptoms (OR 1.32; CI 95% 1.16-1.49) and respiratory disease (OR 1.23; CI 95% 1.07-1.41). Viral load did not differ by SARS-CoV-2 variant, vaccination status, age, or baseline diagnosis. CONCLUSIONS SARS-CoV-2 RNA loads predict the presence of symptomatic and respiratory diseases. The use of standardized, quantitative methods is feasible, allows for replication, and comparisons across institutions, and has the potential to facilitate consensus quantitative thresholds for risk stratification and treatment.
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Affiliation(s)
- Diego R Hijano
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jose A Ferrolino
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Zhengming Gu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jessica N Brazelton
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Haiqing Zhu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Sri Suganda
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Heather L Glasgow
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ronald H Dallas
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Kim J Allison
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Maron
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Himani Darji
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Li Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Thomas P Fabrizio
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Richard J Webby
- Departments of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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Khorraminejad-Shirazi M, Nabavizadeh SS, Aminnia S, Ahmadifar M, Borazjani R, Sadeghi E, Izadpanah S, Heidari Esfahani M, Mokhtari M, Monabati A. Association of Demographic, Clinical, and Vaccination Characteristics with COVID-19 Viral Load Assessed by qRT-PCR. ARCHIVES OF IRANIAN MEDICINE 2023; 26:688-694. [PMID: 38431949 PMCID: PMC10915925 DOI: 10.34172/aim.2023.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/19/2023] [Indexed: 03/05/2024]
Abstract
BACKGROUND The effect of vaccination on the SARS-CoV-2 baseline viral load and clearance during COVID-19 infection is debatable. This study aimed to assess the effects of demographic and vaccination characteristics on the viral load of SARS-CoV-2. METHODS We included the patients referred for outpatient SARS-CoV-2 qRT-PCR (reverse transcriptase quantitative polymerase chain reaction) test between July and September 2022. Cycle threshold (Ct) data were compared based on the demographic and vaccination characteristics. A generalized linear model was used to determine the factors associated with the SARS-CoV-2 PCR Ct value. RESULTS Of 657 participants, 390 (59.4%) were symptomatic and 308 (47.1%) were COVID-19 positive. Among 590 individuals with known vaccination status, 358 (60.6%) were booster vaccinated, 193 (32.6%) were fully vaccinated, 13 (2.2%) were partially vaccinated, and 26 (4.4%) were unvaccinated. Most vaccinated patients received inactivated vaccines (70.5%). The median Ct value was 20 [IQR: 18-23.75] with no significant difference between individuals with different vaccination statuses (P value = 0.182). There were significant differences in Ct value in terms of both symptom presence and onset (both P values < 0.001). Our regression model showed that inactivated vaccines (P value = 0.027), mRNA vaccines (P value = 0.037), and the presence and onset of symptoms (both P values < 0.001) were independent factors significantly associated with the viral load. CONCLUSION The SARS-CoV-2 baseline viral load is unaffected by vaccination status, yet vaccination might accelerate viral clearance. Furthermore, we demonstrated that the presence and onset of symptoms are independent variables substantially associated with the patient's viral load.
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Affiliation(s)
- Mohammadhossein Khorraminejad-Shirazi
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Cell and Molecular Medicine Student Research Group, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Sadat Nabavizadeh
- Otolaryngology Research Center, Department of Otolaryngology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Aminnia
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Ahmadifar
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Roham Borazjani
- Trauma Research Center, Shahid Rajaee (Emtiaz) Trauma Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Erfan Sadeghi
- Research Consultation Center (RCC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shabnam Izadpanah
- Shiraz Transplant Center, Abu-Ali Sina Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Maral Mokhtari
- Raz Pathobiology and Genetic Laboratory, Shiraz, Iran
- Pathology Department, Shahid Faghihi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Monabati
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Raz Pathobiology and Genetic Laboratory, Shiraz, Iran
- Pathology Department, Shahid Faghihi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
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Gomez F, Mehra A, Ensrud E, Diedrich D, Laudanski K. COVID-19: a modern trigger for Guillain-Barre syndrome, myasthenia gravis, and small fiber neuropathy. Front Neurosci 2023; 17:1198327. [PMID: 37712090 PMCID: PMC10498773 DOI: 10.3389/fnins.2023.1198327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/31/2023] [Indexed: 09/16/2023] Open
Abstract
COVID-19 infection has had a profound impact on society. During the initial phase of the pandemic, there were several suggestions that COVID-19 may lead to acute and protracted neurologic sequelae. For example, peripheral neuropathies exhibited distinctive features as compared to those observed in critical care illness. The peripheral nervous system, lacking the protection afforded by the blood-brain barrier, has been a particular site of sequelae and complications subsequent to COVID-19 infection, including Guillain-Barre syndrome, myasthenia gravis, and small fiber neuropathy. We will discuss these disorders in terms of their clinical manifestations, diagnosis, and treatment as well as the pathophysiology in relation to COVID-19.
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Affiliation(s)
- Francisco Gomez
- Department of Neurology, University of Missouri, Columbia, MO, United States
| | - Ashir Mehra
- Department of Neurology, University of Missouri, Columbia, MO, United States
| | - Erik Ensrud
- Department of Neurology, University of Missouri, Columbia, MO, United States
| | - Daniel Diedrich
- Department of Anesthesiology and Perioperative Care, Mayo Clinic, Rochester, MN, United States
| | - Krzysztof Laudanski
- Department of Anesthesiology and Perioperative Care, Mayo Clinic, Rochester, MN, United States
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Silva SJRD, Kohl A, Pena L, Pardee K. Clinical and laboratory diagnosis of monkeypox (mpox): Current status and future directions. iScience 2023; 26:106759. [PMID: 37206155 PMCID: PMC10183700 DOI: 10.1016/j.isci.2023.106759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
The emergence and rapid spread of the monkeypox virus (MPXV) to non-endemic countries has brought this once obscure pathogen to the forefront of global public health. Given the range of conditions that cause similar skin lesions, and because the clinical manifestation may often be atypical in the current mpox outbreak, it can be challenging to diagnose patients based on clinical signs and symptoms. With this perspective in mind, laboratory-based diagnosis assumes a critical role for the clinical management, along with the implementation of countermeasures. Here, we review the clinical features reported in mpox patients, the available laboratory tests for mpox diagnosis, and discuss the principles, advances, advantages, and drawbacks of each assay. We also highlight the diagnostic platforms with the potential to guide ongoing clinical response, particularly those that increase diagnostic capacity in low- and middle-income countries. With the outlook of this evolving research area, we hope to provide a resource to the community and inspire more research and the development of diagnostic alternatives with applications to this and future public health crises.
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Affiliation(s)
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lindomar Pena
- Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto ON M5S 3M2, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto ON M5S 3G8, Canada
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Ravindran S, Gubbay JB, Cronin K, Sullivan A, Zygmunt A, Johnson K, Buchan SA, Parpia AS. Association Between Cycle Threshold Value and Vaccination Status Among Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Cases in Ontario, Canada, in December 2021. Open Forum Infect Dis 2023; 10:ofad282. [PMID: 37274182 PMCID: PMC10234392 DOI: 10.1093/ofid/ofad282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/18/2023] [Indexed: 06/06/2023] Open
Abstract
Background Increased immune evasion by emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and occurrence of breakthrough infections raise questions about whether coronavirus disease 2019 vaccination status affects SARS-CoV-2 viral load among those infected. This study examined the relationship between cycle threshold (Ct) value, which is inversely associated with viral load, and vaccination status at the onset of the Omicron wave onset in Ontario, Canada. Methods Using linked provincial databases, we compared median Ct values across vaccination status among polymerase chain reaction-confirmed Omicron variant SARS-CoV-2 cases (sublineages B.1.1.529, BA.1, and BA.1.1) between 6 and 30 December 2021. Cases were presumed to be Omicron based on S-gene target failure. We estimated the relationship between vaccination status and Ct values using multiple linear regression, adjusting for age group, sex, and symptom status. Results Of the 27 029 presumed Omicron cases in Ontario, the majority were in individuals who had received a complete vaccine series (87.7%), followed by unvaccinated individuals (8.1%), and those who had received a booster dose (4.2%). The median Ct value for post-booster dose individuals (18.3 [interquartile range, 15.4-22.3]) was significantly higher than that for unvaccinated (17.9 [15.2-21.6]; P = .02) and post-vaccine series individuals (17.8 [15.3-21.5]; P = .005). Post-booster dose cases remained associated with a significantly higher median Ct value than cases in unvaccinated individuals (P ≤ .001), after adjustment for covariates. Compared with values in persons aged 18-29 years, Ct values were significantly lower among most age groups >50 years. Conclusions While slightly lower Ct values were observed among unvaccinated individuals infected with Omicron compared with post-booster dose cases, further research is required to determine whether a significant difference in secondary transmission exists between these groups.
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Affiliation(s)
| | - Jonathan B Gubbay
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology and Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Kirby Cronin
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - Ashleigh Sullivan
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - Austin Zygmunt
- Health Protection, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology and Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Canada
| | - Karen Johnson
- Health Protection, Public Health Ontario, Toronto, Ontario, Canada
| | - Sarah A Buchan
- Correspondence: Sarah A. Buchan, Public Health Ontario, 661 University Ave, Floor 17, Toronto, ON M5G 1M1, Canada (); Alyssa S. Parpia, Public Health Ontario, 480 University Ave, Toronto, ON M5G 1V2, Canada ()
| | - Alyssa S Parpia
- Correspondence: Sarah A. Buchan, Public Health Ontario, 661 University Ave, Floor 17, Toronto, ON M5G 1M1, Canada (); Alyssa S. Parpia, Public Health Ontario, 480 University Ave, Toronto, ON M5G 1V2, Canada ()
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Yoo SJ, Kurokawa A, Matsunaga K, Ito K. Spatial distributions of airborne transmission risk on commuter buses: Numerical case study using computational fluid and particle dynamics with computer-simulated persons. EXPERIMENTAL AND COMPUTATIONAL MULTIPHASE FLOW 2023; 5:304-318. [PMID: 36788805 PMCID: PMC9912221 DOI: 10.1007/s42757-022-0146-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/27/2022] [Accepted: 09/07/2022] [Indexed: 02/12/2023]
Abstract
Commuter buses have a high passenger density relative to the interior cabin volume, and it is difficult to maintain a physical/social distance in terms of airborne transmission control. Therefore, it is important to quantitatively investigate the impact of ventilation and air-conditioning in the cabin on the airborne transmission risk for passengers. In this study, comprehensive coupled numerical simulations using computational fluid and particle dynamics (CFPD) and computer-simulated persons (CSPs) were performed to investigate the heterogeneous spatial distribution of the airborne transmission risk in a commuter bus environment under two types of layouts of the ventilation system and two types of passenger densities. Through a series of particle transmission analysis and infection risk assessment in this study, it was revealed that the layout of the supply inlet/exhaust outlet openings of a heating, ventilation, and air-conditioning (HVAC) system has a significant impact on the particle dispersion characteristics inside the bus cabin, and higher infection risks were observed near the single exhaust outlet in the case of higher passenger density. The integrated analysis of CFPD and CSPs in a commuter bus cabin revealed that the airborne transmission risk formed significant heterogeneous spatial distributions, and the changes in air-conditioning conditions had a certain impact on the risk.
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Affiliation(s)
- Sung-Jun Yoo
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka, 816-8580 Japan
| | - Akira Kurokawa
- Interdisciplinary Graduate School of Engineering Science, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka, 816-8580 Japan
| | - Kazuhiko Matsunaga
- Kanagawa Prefectural Junior College for Industrial Technology, 2-4-1 Nakao, Asahi-ku, Yokohama, Kanagawa, 241-0815 Japan
| | - Kazuhide Ito
- Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka, 816-8580 Japan
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Silva SJRD, Kohl A, Pena L, Pardee K. Recent insights into SARS-CoV-2 omicron variant. Rev Med Virol 2023; 33:e2373. [PMID: 35662313 PMCID: PMC9347414 DOI: 10.1002/rmv.2373] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/25/2022] [Accepted: 05/18/2022] [Indexed: 01/28/2023]
Abstract
The SARS-CoV-2 omicron variant (B.1.1.529) was first identified in Botswana and South Africa, and its emergence has been associated with a steep increase in the number of SARS-CoV-2 infections. The omicron variant has subsequently spread very rapidly across the world, resulting in the World Health Organization classification as a variant of concern on 26 November 2021. Since its emergence, great efforts have been made by research groups around the world that have rapidly responded to fill our gaps in knowledge for this novel variant. A growing body of data has demonstrated that the omicron variant shows high transmissibility, robust binding to human angiotensin-converting enzyme 2 receptor, attenuated viral replication, and causes less severe disease in COVID-19 patients. Further, the variant has high environmental stability, high resistance against most therapeutic antibodies, and partial escape neutralisation by antibodies from convalescent patients or vaccinated individuals. With the pandemic ongoing, there is a need for the distillation of literature from primary research into an accessible format for the community. In this review, we summarise the key discoveries related to the SARS-CoV-2 omicron variant, highlighting the gaps in knowledge that guide the field's ongoing and future work.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,Department of Virology, Laboratory of Virology and Experimental Therapy (LAVITE), Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lindomar Pena
- Department of Virology, Laboratory of Virology and Experimental Therapy (LAVITE), Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), Recife, Pernambuco, Brazil
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
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8
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Conjunctival Swabs Reveal Higher Detection Rate Compared to Schirmer Strips for SARS-CoV-2 RNA Detection in Tears of Hospitalized COVID-19 Patients. J Clin Med 2022; 11:jcm11236929. [PMID: 36498504 PMCID: PMC9737489 DOI: 10.3390/jcm11236929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/15/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
Purpose: To determine the prevalence of SARS-CoV-2 in tear samples and to investigate whether it correlates with ocular findings and patients’ prognosis in Brazil. Methods: Tears were collected using Schirmer strips (SS) and conjunctival swabs (CS) from patients hospitalized with laboratory-confirmed SARS-CoV-2 infection. Samples were analyzed using qRT-PCR. Demographic and clinical data, ocular symptoms, and Schirmer tests (ST) were collected from patients. Charlson Comorbidity Index (CCI) was used to rate comorbidities, and patients were monitored until hospital discharge or death. Results: There were 61 hospitalized patients, 33 of which were diagnosed with COVID-19. Within the confirmed COVID-19 patients, SARS-CoV-2 was detected in 18.2% (n = 6) of CS and 12.1% (n = 4) of SS samples. Subjective and objective parameters for dry eye syndrome (e.g., ST COVID-19: 8.3 ± 6.4mm, non-COVID-19: 8.9 ± 6.6mm, p > 0.05) were comparable between COVID-19 (n = 33) and non-COVID-19 patients (n = 28). Among the 16 COVID-19 patients exhibiting ocular symptoms, only tearing was reported significantly more frequently when tear samples were positive for SARS-CoV-2 (p < 0.05). Strikingly, patients whose tears tested positive for SARS-CoV-2 had significantly inferior CCI (pos.: 34.0 ± 31.8%, neg.: 67.6 ± 36.4%, p < 0.05) and higher mortality rates (pos.: 50.0%, neg.: 7.4%, p < 0.01). Conclusions: SARS-CoV-2 was detected with a prevalence of 18.2% on the ocular surface. Decreased CCI and increased mortality rate in the positive tear group suggests that viral detection may relate to prognosis and highlight the need of personal protective measures for healthcare professionals. Most of the patients, regardless of COVID-19 diagnosis, had low tear production and eye discomfort, possibly pointing to the need for artificial tear use during hospitalization.
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da Silva SJR. The emergence of new SARS-CoV-2 omicron subvariants introduces uncertainty about the end of the COVID-19 pandemic. Front Med (Lausanne) 2022; 9:1010489. [PMID: 36300185 PMCID: PMC9590648 DOI: 10.3389/fmed.2022.1010489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
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da Silva SJR, do Nascimento JCF, Germano Mendes RP, Guarines KM, Targino Alves da Silva C, da Silva PG, de Magalhães JJF, Vigar JRJ, Silva-Júnior A, Kohl A, Pardee K, Pena L. Two Years into the COVID-19 Pandemic: Lessons Learned. ACS Infect Dis 2022; 8:1758-1814. [PMID: 35940589 PMCID: PMC9380879 DOI: 10.1021/acsinfecdis.2c00204] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.
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Affiliation(s)
- Severino Jefferson Ribeiro da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Jessica Catarine Frutuoso do Nascimento
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Renata Pessôa Germano Mendes
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Klarissa Miranda Guarines
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Caroline Targino Alves da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Poliana Gomes da Silva
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
| | - Jurandy Júnior Ferraz de Magalhães
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil.,Department of Virology, Pernambuco State Central Laboratory (LACEN/PE), 52171-011 Recife, Pernambuco, Brazil.,University of Pernambuco (UPE), Serra Talhada Campus, 56909-335 Serra Talhada, Pernambuco, Brazil.,Public Health Laboratory of the XI Regional Health, 56912-160 Serra Talhada, Pernambuco, Brazil
| | - Justin R J Vigar
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Abelardo Silva-Júnior
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), 57072-900 Maceió, Alagoas, Brazil
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, United Kingdom
| | - Keith Pardee
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Lindomar Pena
- Laboratory of Virology and Experimental Therapy (LAVITE), Department of Virology, Aggeu Magalhães Institute (IAM), Oswaldo Cruz Foundation (Fiocruz), 50670-420 Recife, Pernambuco, Brazil
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11
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Batista-Roche JL, Gómez-Gil B, Lund G, Berlanga-Robles CA, García-Gasca A. Global m6A RNA Methylation in SARS-CoV-2 Positive Nasopharyngeal Samples in a Mexican Population: A First Approximation Study. EPIGENOMES 2022; 6:epigenomes6030016. [PMID: 35893012 PMCID: PMC9326742 DOI: 10.3390/epigenomes6030016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/11/2022] [Accepted: 06/20/2022] [Indexed: 02/05/2023] Open
Abstract
The Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the causal agent of COVID-19 (Coronavirus Disease-19). Both mutation and/or recombination events in the SARS-CoV-2 genome have resulted in variants that differ in transmissibility and severity. Furthermore, RNA methylation of the N6 position of adenosine (m6A) is known to be altered in cells infected with SARS-CoV-2. However, it is not known whether this epitranscriptomic modification differs across individuals dependent on the presence of infection with distinct SARS-CoV-2 variants, the viral load, or the vaccination status. To address this issue, we selected RNAs (n = 60) from SARS-CoV-2 sequenced nasopharyngeal samples (n = 404) of 30- to 60-year-old outpatients or hospitalized individuals from the city of Mazatlán (Mexico) between February 2021 and March 2022. Control samples were non-infected individuals (n = 10). SARS-CoV-2 was determined with real-time PCR, viral variants were determined with sequencing, and global m6A levels were determined by using a competitive immunoassay method. We identified variants of concern (VOC; alpha, gamma, delta, omicron), the variant of interest (VOI; epsilon), and the lineage B.1.1.519. Global m6A methylation differed significantly across viral variants (p = 3.2 × 10−7). In particular, we found that m6A levels were significantly lower in the VOC delta- and omicron-positive individuals compared to non-infected individuals (p = 2.541236 × 10−2 and 1.134411 × 10−4, respectively). However, we uncovered no significant correlation between global m6A levels and viral nucleocapsid (N) gene expression or age. Furthermore, individuals with complete vaccination schemes showed significantly lower m6A levels than unvaccinated individuals (p = 2.6 × 10−4), and differences in methylation levels across variants in unvaccinated individuals were significant (p = 3.068 × 10−3). These preliminary results suggest that SARS-CoV-2 variants show differences in global m6A levels.
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Affiliation(s)
- Jorge Luis Batista-Roche
- Molecular and Cellular Biology, Centro de Investigación en Alimentación y Desarrollo, Mazatlán 82112, Mexico;
| | - Bruno Gómez-Gil
- Microbial Genomics, Centro de Investigación en Alimentación y Desarrollo, Mazatlán 82112, Mexico;
| | - Gertrud Lund
- Department of Genetic Engineering, CINVESTAV Irapuato Unit, Irapuato 36821, Mexico;
| | | | - Alejandra García-Gasca
- Molecular and Cellular Biology, Centro de Investigación en Alimentación y Desarrollo, Mazatlán 82112, Mexico;
- Correspondence: ; Tel.: +52-669-989-8700
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[Overview of COVID-19 vaccines licensed in the EU-from technology via clinical trial to registration]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2022; 65:1237-1243. [PMID: 36257986 PMCID: PMC9579648 DOI: 10.1007/s00103-022-03600-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022]
Abstract
Currently (as of July 2022), six different COVID-19 vaccines are licensed in the EU. These include two mRNA-based vaccines (BNT162b2, Comirnaty® and mRNA-1273, Spikevax®), two adenoviral vector-based vaccines (AZD1222, Vaxzevria® and Ad26.COV2.S, Jcovden®), the subunit vaccine Nuvaxovid® (NVX-CoV2373), and the inactivated virus vaccine VLA2001. Although these vaccines are based on different technologies, they all share the use of the spike protein of SARS-CoV‑2 as antigen.This overview describes the characteristics of their composition, their efficacy, and the impact of various factors on efficacy. Another aspect of this overview is the description of the approval process and the identification of factors that have contributed to the unprecedented speed in the development and approval of vaccines against a pandemic pathogen.
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