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Jemmieh K, Tawengi M, Alyaarabi T, Hassona A, Ghoul I, Al Abdulla S, Elzawawi KE, Karen O, Doi SA, Chivese T. No Association Between Ct Value and COVID-19 Severity and Mortality in Qatar. Int J Gen Med 2023; 16:5323-5331. [PMID: 38021068 PMCID: PMC10658937 DOI: 10.2147/ijgm.s404696] [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: 01/23/2023] [Accepted: 07/13/2023] [Indexed: 12/01/2023] Open
Abstract
Background The association between the cycle threshold (Ct) which reflects the SARS-CoV-2 viral load and the severity of COVID-19 is still not clear. We investigated the association between Ct values, symptoms and the risk of ICU admission and mortality from COVID-19 in Qatar. Methods This case-control study used data of hospitalized individuals with confirmed COVID-19 during the period March to September 2020. Cases were defined as individuals with confirmed COVID-19 who were admitted to the intensive care unit (ICU) or died and controls as those who were not admitted to the ICU. The association between Ct value, symptoms, ICU admission and mortality was investigated using Ct value as a categorical variable (below and above 25) in multivariable regression models and adjusted for relevant confounders. Results A total of 622 participants with median age 53 (IQR: 53-63), of which 69% were males, were included. There were 236 ICU admissions and 111 deaths. When categorized, Ct value (<25 vs ≥25) had no association with the odds of ICU admission (OR 0.85, 95% CI 0.56 to 1.29) or odds of mortality (OR 1.21, 95% CI 0.71 to 2.08). Respiratory (OR 2.95, 95% CI 1.57 to 5.56) and gastrointestinal symptoms (OR 1.99, 95% CI 1.18 to 3.35) were associated with higher odds of ICU admission. Similarly, respiratory (OR 4.96, 95% CI 1.10 to 22.43) and gastrointestinal symptoms (OR 3.17, 95% CI 1.29 to 7.84) were associated with higher odds of mortality. Conclusion Although RT-PCR Ct has good diagnostic value, its prognostic value appears to be unreliable. Respiratory and gastrointestinal symptoms are associated with COVID-19 criticality and mortality in this setting.
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Affiliation(s)
- Khaleed Jemmieh
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Mohamed Tawengi
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Tamader Alyaarabi
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Aseel Hassona
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ikhlas Ghoul
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Sara Al Abdulla
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Khaled E Elzawawi
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Omar Karen
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Suhail A Doi
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Tawanda Chivese
- Department of Population Medicine, College of Medicine, QU Health, Qatar University, Doha, Qatar
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2
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Nasrallah GK, Ali F, Younes S, Al Khatib HA, Al-Thani AA, Yassine HM. Enhancing the sensitivity of rapid antigen detection test (RADT) of different SARS-CoV-2 variants and lineages using fluorescence-labeled antibodies and a fluorescent meter. Heliyon 2023; 9:e17179. [PMID: 37325455 PMCID: PMC10257515 DOI: 10.1016/j.heliyon.2023.e17179] [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: 12/12/2022] [Revised: 05/21/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023] Open
Abstract
RT-qPCR is considered the gold standard for diagnosis of COVID-19; however, it is laborious, time-consuming, and expensive. RADTs have evolved recently as relatively inexpensive methods to address these shortcomings, but their performance for detecting different SARS-COV-2 variants remains limited. RADT test performance could be enhanced using different antibody labeling and signal detection techniques. Here, we aimed to evaluate the performance of two antigen RADTs for detecting different SARS-CoV-2 variants: (i) the conventional colorimetric RADT (Ab-conjugated with gold beads); and (ii) the new Finecare™ RADT (Ab-coated fluorescent beads). Finecare™ is a meter used for the detection of a fluorescent signal. 187 frozen nasopharyngeal swabs collected in Universal transport (UTM) that are RT-qPCR positive for different SARS-CoV-2 variants were selected, including Alpha (n = 60), Delta (n = 59), and Omicron variants (n = 108). Sixty flu and 60 RSV-positive samples were included as negative controls (total sample number = 347). The conventional RADT showed sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 62.4% (95%CI: 54-70), 100% (95%CI: 97-100), 100% (95%CI: 100-100), and 58% (95%CI: 49-67), respectively. These measurements were enhanced using the Finecare™ RADT: sensitivity, specificity, PPV, and NPV were 92.6% (95%CI: 89.08-92.3), 96% (95%CI: 96-99.61), 98% (95%CI: 89-92.3), and 85% (95%CI: 96-99.6) respectively. The sensitivity of both RADTs could be greatly underestimated because nasopharyngeal swab samples collected UTM and stored at -80 °C were used. Despite that, our results indicate that the Finecare™ RADT is appropriate for clinical laboratory and community-based surveillance due to its high sensitivity and specificity.
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Affiliation(s)
- Gheyath K Nasrallah
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar
- Biomedical Sciences Department, College of Health Sciences, Qatar University, Doha, 2713, Qatar
| | - Fatma Ali
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar
- Biomedical Sciences Department, College of Health Sciences, Qatar University, Doha, 2713, Qatar
| | - Salma Younes
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar
- Biomedical Sciences Department, College of Health Sciences, Qatar University, Doha, 2713, Qatar
| | | | | | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar
- Biomedical Sciences Department, College of Health Sciences, Qatar University, Doha, 2713, Qatar
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3
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De Nardo P, Tebon M, Savoldi A, Soriolo N, Danese E, Peserico D, Morra M, Gentilotti E, Caliskan G, Marchetti P, Cecchetto R, Mazzariol A, Verlato G, Gibellini D, Tacconelli E. Diagnostic Accuracy of a Rapid SARS-CoV-2 Antigen Test Among People Experiencing Homelessness: A Prospective Cohort and Implementation Study. Infect Dis Ther 2023; 12:1073-1082. [PMID: 36907951 PMCID: PMC10008716 DOI: 10.1007/s40121-023-00787-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
INTRODUCTION Detection strategies in vulnerable populations such as people experiencing homelessness (PEH) need to be explored to promptly recognize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks. This study investigated the diagnostic accuracy of a rapid SARS-CoV-2 Ag test in PEH during two pandemic waves compared with gold standard real-time multiplex reverse transcription polymerase chain reaction (rtRT-PCR). METHODS All PEH ≥ 18 years requesting residence at the available shelters in Verona, Italy, across two cold-weather emergency periods (November 2020-May 2021 and December 2021-April 2022) were prospectively screened for SARS-CoV-2 infection by means of a naso-pharyingeal swab. A lateral flow immunochromatographic assay (Biocredit® COVID-19 Ag) was used as antigen-detecting rapid diagnostic test (Ag-RDT). The rtRT-PCR was performed with Allplex™ SARS-CoV-2 assay kit (Seegene). Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated as measures for diagnostic accuracy. RESULTS Overall, 503 participants were enrolled during the two intervention periods for a total of 732 paired swabs collected: 541 swabs in the first period and 191 in the second. No significant differences in demographic and infection-related characteristics were observed in tested subjects in the study periods, except for the rate of previous infection (0.8% versus 8%; p < 0.001) and vaccination (6% versus 73%; p < 0.001). The prevalence of SARS-CoV-2 in the cohort was 8% (58/732 swabs positive with rtRT-PCR). Seventeen swabs were collected from symptomatic patients (7%). Among them, the concordance between rtRT-PCR and Ag-RDT was 100%, 7 (41.2%) positive and 10 negative pairs. The overall sensitivity of Ag-RDT was 63.8% (95% CI 60.3-67.3) and specificity was 99.8% (95% CI 99.6-100). PPV and NPV were 97.5% and 96.8%, respectively. Sensitivity and specificity did not change substantially across the two periods (65.1% and 99.8% in 2020-2021 vs. 60% and 100% in 2021-2022). CONCLUSIONS A periodic Ag-RDT-based screening approach for PEH at point of care could guide preventive measures, including prompt isolation, without referral to hospital-based laboratories for molecular test confirmation in case of positive detection even in individuals asymptomatic for COVID-19. This could help reduce the risk of outbreaks in shelter facilities.
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Affiliation(s)
- Pasquale De Nardo
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy.
| | - Maela Tebon
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Alessia Savoldi
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Nicola Soriolo
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Elisa Danese
- Clinical Biochemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Denise Peserico
- Clinical Biochemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Matteo Morra
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Elisa Gentilotti
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Gulser Caliskan
- Unit of Epidemiology & Medical Statistics, Department of Diagnostics and Public Health, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Pierpaolo Marchetti
- Unit of Epidemiology & Medical Statistics, Department of Diagnostics and Public Health, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Riccardo Cecchetto
- Microbiology and Virology Section, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Annarita Mazzariol
- Microbiology and Virology Section, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Giuseppe Verlato
- Unit of Epidemiology & Medical Statistics, Department of Diagnostics and Public Health, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Davide Gibellini
- Microbiology and Virology Section, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134, Verona, Italy
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Qassim SH, Hasan MR, Tang P, Chemaitelly H, Ayoub HH, Yassine HM, Al-Khatib HA, Smatti MK, Abdul-Rahim HF, Nasrallah GK, Al-Kuwari MG, Al-Khal A, Coyle P, Gillani I, Kaleeckal AH, Shaik RM, Latif AN, Al-Kuwari E, Jeremijenko A, Butt AA, Bertollini R, Al-Romaihi HE, Al-Thani MH, Abu-Raddad LJ. Effects of SARS-CoV-2 Alpha, Beta, and Delta variants, age, vaccination, and prior infection on infectiousness of SARS-CoV-2 infections. Front Immunol 2022; 13:984784. [PMID: 36177014 PMCID: PMC9513583 DOI: 10.3389/fimmu.2022.984784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
In 2021, Qatar experienced considerable incidence of SARS-CoV-2 infection that was dominated sequentially by the Alpha, Beta, and Delta variants. Using the cycle threshold (Ct) value of an RT-qPCR-positive test to proxy the inverse of infectiousness, we investigated infectiousness of SARS-CoV-2 infections by variant, age, sex, vaccination status, prior infection status, and reason for testing in a random sample of 18,355 RT-qPCR-genotyped infections. Regression analyses were conducted to estimate associations with the Ct value of RT-qPCR-positive tests. Compared to Beta infections, Alpha and Delta infections demonstrated 2.56 higher Ct cycles (95% CI: 2.35-2.78), and 4.92 fewer cycles (95% CI: 4.67- 5.16), respectively. The Ct value declined gradually with age and was especially high for children <10 years of age, signifying lower infectiousness in small children. Children <10 years of age had 2.18 higher Ct cycles (95% CI: 1.88-2.48) than those 10-19 years of age. Compared to unvaccinated individuals, the Ct value was higher among individuals who had received one or two vaccine doses, but the Ct value decreased gradually with time since the second-dose vaccination. Ct value was 2.07 cycles higher (95% CI: 1.42-2.72) for those with a prior infection than those without prior infection. The Ct value was lowest among individuals tested because of symptoms and was highest among individuals tested as a travel requirement. Delta was substantially more infectious than Beta. Prior immunity, whether due to vaccination or prior infection, is associated with lower infectiousness of breakthrough infections, but infectiousness increases gradually with time since the second-dose vaccination.
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Affiliation(s)
- Suelen H. Qassim
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
- World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine–Qatar, Cornell University, Qatar Foundation – Education City, Doha, Qatar
- Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | | | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Hiam Chemaitelly
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
- World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine–Qatar, Cornell University, Qatar Foundation – Education City, Doha, Qatar
- Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Houssein H. Ayoub
- Mathematics Program, Department of Mathematics, Statistics, and Physics, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hadi M. Yassine
- Biomedical Research Center, QU Health, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hebah A. Al-Khatib
- Biomedical Research Center, QU Health, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Maria K. Smatti
- Biomedical Research Center, QU Health, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hanan F. Abdul-Rahim
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Gheyath K. Nasrallah
- Biomedical Research Center, QU Health, Qatar University, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | | | | | - Peter Coyle
- Biomedical Research Center, QU Health, Qatar University, Doha, Qatar
- Hamad Medical Corporation, Doha, Qatar
- Wellcome-Wolfson Institute for Experimental Medicine, Queens University, Belfast, United Kingdom
| | | | | | | | | | | | | | - Adeel A. Butt
- Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States
- Hamad Medical Corporation, Doha, Qatar
- Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | | | | | | | - Laith J. Abu-Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
- World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine–Qatar, Cornell University, Qatar Foundation – Education City, Doha, Qatar
- Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
- *Correspondence: Laith J. Abu-Raddad,
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Motahhar M, Keyvanfar H, Shoushtari A, Fallah Mehrabadi MH, Nikbakht Brujeni G. The arrival of highly pathogenic avian influenza viruses H5N8 in Iran through two windows, 2016. Virus Genes 2022; 58:527-539. [PMID: 36098944 DOI: 10.1007/s11262-022-01930-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022]
Abstract
The highly pathogenic avian influenza (HPAI) H5N1 virus has received considerable attention during the past 2 decades due to its zoonotic and mutative features. This Virus is of special importance due to to the possibility of causing infection in human populations. According to it's geographical location, Iran hosts a large number of aquatic migratory birds every year, and since these birds can be considered as the host of the H5 HPAI, the country is significantly at risk of this virus. the In this study, the molecular characteristics of hemagglutinin (HA) and neuraminidase (NA) genes of the H5N8 strain were identified in Malard county of Tehran province and Meighan wetland of Arak city, Markazi province were investigated. Based on the analysis of the amino acid sequence of the HA genes, the cleavage site of the gene includes the PLREKRRKR/GLF polybasic amino acid motif, which is a characteristic of highly pathogenic influenza viruses. The HA gene of two viruses had T156A, S123P, S133A mutations associated with the increased mammalian sialic acid-binding, and the NA gene of two viruses had H253Y mutations associated with the resistance to antiviral drugs. Phylogenetic analysis of the HA genes indicated the classification of these viruses in the 2.3.4.4 b subclade. Although the A/Goose/Iran/180/2016 virus was also an H5N8 2.3.4.4 b virus, its cluster was separated from the A/Chicken/Iran/162/2016 virus. This means that the entry of these viruses in to the country happened through more than one window. Furthermore, it seems that the introduction of these H5N8 HPAI strains in Iran probably occurred through the West Asia-East African flyway by wild migratory aquatic birds.
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Affiliation(s)
- Minoo Motahhar
- Department of Pathobiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hadi Keyvanfar
- Department of Pathobiology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Abdolhamid Shoushtari
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Mohammad Hossein Fallah Mehrabadi
- Department of Avian Diseases Research and Diagnostics, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran
| | - Gholamreza Nikbakht Brujeni
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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