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Embekkat Kaviyil J, Raja K, Gaitonde R, Easwaran S, Kala V K, Korol Ponnambath D. Targeted Sanger Sequencing of a Cluster of COVID-19 Cases in the Surgical ICU of a Non-COVID Hospital: Lessons Learned. Cureus 2023; 15:e44755. [PMID: 37809129 PMCID: PMC10556540 DOI: 10.7759/cureus.44755] [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] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
Small clusters of infection due to SARS-CoV-2 in a non-COVID-19 healthcare facility can disrupt services. Here, we investigated a cluster of SARS-CoV-2 cases by targeted Sanger sequencing and clinical epidemiological methods in a non-COVID-19 super-specialty hospital. Epidemiological data were collected in a blinded manner using a proforma to find the risk factors associated with infection. Targeted Sanger sequencing of the spike protein receptor binding domain (RBD) coding region was performed on all the available real-time reverse transcription polymerase chain reaction (RT-PCR)-positive samples that included a patient, his mother, and 11 healthcare workers (HCWs) to determine any genomic variations in the samples from the cluster. All positive cases were due to the Delta variant. However, it detected a unique mutation, N501I, in the RBD region of the SARS-CoV-2 strains. The viral genome extracted from the mother's sample lacked the mutation, thus excluding her from the cluster and pointing out that the outbreak was nosocomial, leading to a focus on infection control measures. Though whole genome sequencing is more universally accepted, in this study, targeted sanger sequencing provided a rapid and cost-effective solution to correctly delineate between the actual cases that form the cluster and other community cases in a pandemic situation.
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Affiliation(s)
- Jyothi Embekkat Kaviyil
- Microbiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum, IND
| | - Kavita Raja
- Microbiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum, IND
| | - Rakhal Gaitonde
- Public Health, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum, IND
| | | | - Kumari Kala V
- Nursing, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum, IND
| | - Dinoop Korol Ponnambath
- Microbiology, Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Trivandrum, IND
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Abdaljaleel M, Tawalbeh I, Sallam M, Hani AB, Al-Abdallat IM, Omari BA, Al-Mustafa S, Abder-Rahman H, Abbas AS, Zureigat M, Al-Abbadi MA. Postmortem lung and heart examination of COVID-19 patients in a case series from Jordan. J Pathol Transl Med 2023; 57:102-112. [PMID: 36950812 PMCID: PMC10028009 DOI: 10.4132/jptm.2023.01.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/30/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has emerged as a pandemic for more than 2 years. Autopsy examination is an invaluable tool to understand the pathogenesis of emerging infections and their consequent mortalities. The aim of the current study was to present the lung and heart pathological findings of COVID-19-positive autopsies performed in Jordan. METHODS The study involved medicolegal cases, where the cause of death was unclear and autopsy examination was mandated by law. We included the clinical and pathologic findings of routine gross and microscopic examination of cases that were positive for COVID-19 at time of death. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed through molecular detection by real-time polymerase chain reaction, serologic testing for IgM and electron microscope examination of lung samples. RESULTS Seventeen autopsies were included, with male predominance (76.5%), Jordanians (70.6%), and 50 years as the mean age at time of death. Nine out of 16 cases (56.3%) had co-morbidities, with one case lacking such data. Histologic examination of lung tissue revealed diffuse alveolar damage in 13/17 cases (76.5%), and pulmonary microthrombi in 8/17 cases (47.1%). Microscopic cardiac findings were scarcely detected. Two patients died as a direct result of acute cardiac disease with limited pulmonary findings. CONCLUSIONS The detection of SARS-CoV-2 in postmortem examination can be an incidental or contributory finding which highlights the value of autopsy examination to determine the exact cause of death in controversial cases.
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Affiliation(s)
- Maram Abdaljaleel
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
| | - Isra Tawalbeh
- Department of Forensic Pathology, Ministry of Health, Amman, Jordan
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Amjad Bani Hani
- Department of General Surgery, School of Medicine, The University of Jordan, Amman, Jordan
| | - Imad M Al-Abdallat
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
| | - Baheth Al Omari
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
| | - Sahar Al-Mustafa
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
| | - Hasan Abder-Rahman
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
| | - Adnan Said Abbas
- Department of Forensic Pathology, Ministry of Health, Amman, Jordan
| | - Mahmoud Zureigat
- Department of Forensic Pathology, Ministry of Health, Amman, Jordan
| | - Mousa A Al-Abbadi
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
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Gomari MM, Tarighi P, Choupani E, Abkhiz S, Mohamadzadeh M, Rostami N, Sadroddiny E, Baammi S, Uversky VN, Dokholyan NV. Structural evolution of Delta lineage of SARS-CoV-2. Int J Biol Macromol 2023; 226:1116-1140. [PMID: 36435470 PMCID: PMC9683856 DOI: 10.1016/j.ijbiomac.2022.11.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
One of the main obstacles in prevention and treatment of COVID-19 is the rapid evolution of the SARS-CoV-2 Spike protein. Given that Spike is the main target of common treatments of COVID-19, mutations occurring at this virulent factor can affect the effectiveness of treatments. The B.1.617.2 lineage of SARS-CoV-2, being characterized by many Spike mutations inside and outside of its receptor-binding domain (RBD), shows high infectivity and relative resistance to existing cures. Here, utilizing a wide range of computational biology approaches, such as immunoinformatics, molecular dynamics (MD), analysis of intrinsically disordered regions (IDRs), protein-protein interaction analyses, residue scanning, and free energy calculations, we examine the structural and biological attributes of the B.1.617.2 Spike protein. Furthermore, the antibody design protocol of Rosetta was implemented for evaluation the stability and affinity improvement of the Bamlanivimab (LY-CoV55) antibody, which is not capable of interactions with the B.1.617.2 Spike. We observed that the detected mutations in the Spike of the B1.617.2 variant of concern can cause extensive structural changes compatible with the described variation in immunogenicity, secondary and tertiary structure, oligomerization potency, Furin cleavability, and drug targetability. Compared to the Spike of Wuhan lineage, the B.1.617.2 Spike is more stable and binds to the Angiotensin-converting enzyme 2 (ACE2) with higher affinity.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences, Tehran 1449614535, Iran; Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Parastoo Tarighi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Edris Choupani
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Shadi Abkhiz
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Masoud Mohamadzadeh
- Department of Chemistry, Faculty of Sciences, University of Hormozgan, Bandar Abbas 7916193145, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak 3848177584, Iran
| | - Esmaeil Sadroddiny
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir 43150, Morocco
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 16802, USA.
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Dofuor AK, Quartey NKA, Osabutey AF, Boateng BO, Lutuf H, Osei JHN, Ayivi-Tosuh SM, Aiduenu AF, Ekloh W, Loh SK, Opoku MJ, Aidoo OF. The Global Impact of COVID-19: Historical Development, Molecular Characterization, Drug Discovery and Future Directions. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2023; 16:2632010X231218075. [PMID: 38144436 PMCID: PMC10748929 DOI: 10.1177/2632010x231218075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/16/2023] [Indexed: 12/26/2023]
Abstract
In December 2019, an outbreak of a respiratory disease called the coronavirus disease 2019 (COVID-19) caused by a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in Wuhan, China. The SARS-CoV-2, an encapsulated positive-stranded RNA virus, spread worldwide with disastrous consequences for people's health, economies, and quality of life. The disease has had far-reaching impacts on society, including economic disruption, school closures, and increased stress and anxiety. It has also highlighted disparities in healthcare access and outcomes, with marginalized communities disproportionately affected by the SARS-CoV-2. The symptoms of COVID-19 range from mild to severe. There is presently no effective cure. Nevertheless, significant progress has been made in developing COVID-19 vaccine for different therapeutic targets. For instance, scientists developed multifold vaccine candidates shortly after the COVID-19 outbreak after Pfizer and AstraZeneca discovered the initial COVID-19 vaccines. These vaccines reduce disease spread, severity, and mortality. The addition of rapid diagnostics to microscopy for COVID-19 diagnosis has proven crucial. Our review provides a thorough overview of the historical development of COVID-19 and molecular and biochemical characterization of the SARS-CoV-2. We highlight the potential contributions from insect and plant sources as anti-SARS-CoV-2 and present directions for future research.
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Affiliation(s)
- Aboagye Kwarteng Dofuor
- Department of Biological Sciences, School of Natural and Environmental Sciences, University of Environment and Sustainable Development, Somanya, Ghana
| | - Naa Kwarley-Aba Quartey
- Department of Food Science and Technology, Faculty of Biosciences, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Belinda Obenewa Boateng
- Coconut Research Program, Oil Palm Research Institute, Council for Scientific and Industrial Research, Sekondi-Takoradi, Ghana
| | - Hanif Lutuf
- Crop Protection Division, Oil Palm Research Institute, Council for Scientific and Industrial Research, Kade, Ghana
| | - Joseph Harold Nyarko Osei
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Selina Mawunyo Ayivi-Tosuh
- Department of Biochemistry, School of Life Sciences, Northeast Normal University, Changchun, Jilin Province, China
| | - Albert Fynn Aiduenu
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Accra, Ghana
| | - William Ekloh
- Department of Biochemistry, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Seyram Kofi Loh
- Department of Built Environment, School of Sustainable Development, University of Environment and Sustainable Development, Somanya, Ghana
| | - Maxwell Jnr Opoku
- Department of Biological Sciences, School of Natural and Environmental Sciences, University of Environment and Sustainable Development, Somanya, Ghana
| | - Owusu Fordjour Aidoo
- Department of Biological Sciences, School of Natural and Environmental Sciences, University of Environment and Sustainable Development, Somanya, Ghana
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Qaqish A, Al-Omari M, Abbas MM, Ghazo M. Two years of COVID-19 pandemic in Jordan: A focus on epidemiology and vaccination. J Glob Health 2022; 12:03063. [PMID: 36181720 PMCID: PMC9526477 DOI: 10.7189/jogh.12.03063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Arwa Qaqish
- Department of Biology and Biotechnology, The Hashemite University, Zarqa, Jordan
| | - Mariam Al-Omari
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | - Manal M Abbas
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan.,Pharmacological and Diagnostic Research Lab, Al-Ahliyya Amman University, Amman, Jordan
| | - Mahmoud Ghazo
- Jordan Ministry of Health, Laboratory Directorate, Amman, Jordan
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6
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Parker E, Anderson C, Zeller M, Tibi A, Havens JL, Laroche G, Benlarbi M, Ariana A, Robles-Sikisaka R, Latif AA, Watts A, Awidi A, Jaradat SA, Gangavarapu K, Ramesh K, Kurzban E, Matteson NL, Han AX, Hughes LD, McGraw M, Spencer E, Nicholson L, Khan K, Suchard MA, Wertheim JO, Wohl S, Côté M, Abdelnour A, Andersen KG, Abu-Dayyeh I. Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions. Nat Commun 2022; 13:4784. [PMID: 35970983 PMCID: PMC9376901 DOI: 10.1038/s41467-022-32536-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/04/2022] [Indexed: 01/02/2023] Open
Abstract
Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding in the early pandemic to more regional seeding for the travel restrictions period. We show that land travel, particularly freight transport, drove introduction risk during the travel restrictions period. High regional connectivity and land travel also drove Jordan's export risk. Our findings emphasize regional connectedness and land travel as drivers of transmission in the Middle East.
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Affiliation(s)
- Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ahmad Tibi
- Biolab Diagnostic Laboratories, Amman, Jordan
| | - Jennifer L Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Geneviève Laroche
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Mehdi Benlarbi
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Ardeshir Ariana
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alaa Abdel Latif
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman, Jordan
- Thrombosis, haemostasis laboratory, School of Medicine, The University of Jordan, Amman, Jordan
| | - Saied A Jaradat
- Princess Haya Biotechnology Center, Jordan University of Science and Technology, Irbid, Jordan
| | - Karthik Gangavarapu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karthik Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michelle McGraw
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Scripps Research Translational Institute, La Jolla, CA, USA
| | | | | | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | | | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Issa Abu-Dayyeh
- Biolab Diagnostic Laboratories, Amman, Jordan.
- Cell Therapy Center, The University of Jordan, Amman, Jordan.
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Qaqish B, Sallam M, Al-Khateeb M, Reisdorf E, Mahafzah A. Assessment of COVID-19 Molecular Testing Capacity in Jordan: A Cross-Sectional Study at the Country Level. Diagnostics (Basel) 2022; 12:909. [PMID: 35453957 PMCID: PMC9024853 DOI: 10.3390/diagnostics12040909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic control measures rely on the accurate and timely diagnosis of infected individuals. Real-time polymerase chain reaction (qPCR) remains the gold-standard method for laboratory diagnosis of the disease. Delayed diagnosis due to challenges that face laboratories performing COVID-19 testing can hinder public health control measures. Such challenges may be related to shortages in staff, equipment or materials, improper inventory management, flawed workflow, or long turnaround time (TAT). The aim of the current study was to assess the overall COVID-19 molecular testing capacity in Jordan as of April 2021. In addition, the study’s objectives included the identification of potential defects that could comprise the utility of the COVID-19 molecular testing capacity in the country. All laboratories certified by the Ministry of Health (MoH) in Jordan to conduct molecular testing for SARS-CoV-2 were invited to participate in this study. Data were obtained from the participating laboratories (those which agreed to participate) by either telephone interviews or a self-reported written questionnaire with items assessing the key aspects of COVID-19 molecular testing. The full molecular testing capacity in each laboratory was self-reported considering 24 working hours. The total number of participating laboratories was 51 out of 77 (66.2%), with the majority being affiliated with MoH (n = 17) and private laboratories (n = 20). The total molecular COVID-19 testing capacity among the participating laboratories was estimated at 574,441 tests per week, while the actual highest number of tests performed over a single week was 310,047 (54.0%, reported in March 2021). Laboratories affiliated with the MoH were operating at a level closer to their maximum capacity (87.2% of their estimated full capacity for COVID-19 testing) compared to private hospital laboratories (41.3%, p = 0.004), private laboratories (20.8%, p < 0.001), and academic/research laboratories (14.7%, p < 0.001, ANOVA). The national average daily COVID-19 molecular testing was 349.2 tests per 100,000 people in April 2021. The average TAT over the first week of April 2021 for COVID-19 testing was 932 min among the participating laboratories, with the longest TAT among MoH laboratories (mean: 1959 min) compared to private laboratories (mean: 333 min, p < 0.001). Molecular COVID-19 testing potential in Jordan has not been fully utilized, particularly for private laboratories and those belonging to academic/research centers. Supply-chain challenges and shortages in staff were identified as potential obstacles hindering the exploitation of full molecular testing capacity for COVID-19 in the country.
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Affiliation(s)
- Bara’a Qaqish
- Abt Associates, United States Agency for International Development (USAID) Funded Local Health System Sustainability Project (LHSS), Amman 11822, Jordan;
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22184 Malmo, Sweden
| | | | - Erik Reisdorf
- Infectious Disease Detection and Surveillance (IDDS), Rockville, MD 20894, USA;
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
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8
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Chouikha A, Fares W, Laamari A, Haddad-Boubaker S, Belaiba Z, Ghedira K, Kammoun Rebai W, Ayouni K, Khedhiri M, Ben Halima S, Krichen H, Touzi H, Ben Dhifallah I, Guerfali FZ, Atri C, Azouz S, Khamessi O, Ardhaoui M, Safer M, Ben Alaya N, Guizani I, Kefi R, Gdoura M, Triki H. Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19. Viruses 2022; 14:624. [PMID: 35337031 PMCID: PMC8956073 DOI: 10.3390/v14030624] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 12/17/2022] Open
Abstract
Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.
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Affiliation(s)
- Anissa Chouikha
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Wasfi Fares
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Asma Laamari
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
| | - Sondes Haddad-Boubaker
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Zeineb Belaiba
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia;
| | - Wafa Kammoun Rebai
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia; (W.K.R.); (R.K.)
| | - Kaouther Ayouni
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Marwa Khedhiri
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Samar Ben Halima
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
| | - Henda Krichen
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
| | - Henda Touzi
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Imen Ben Dhifallah
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Fatma Z. Guerfali
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII) (LR16IPT02), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia; (F.Z.G.); (C.A.)
| | - Chiraz Atri
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII) (LR16IPT02), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia; (F.Z.G.); (C.A.)
| | - Saifeddine Azouz
- Genomics Plateform, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia;
| | - Oussema Khamessi
- Laboratoire de Venins et Biomolécules Thérapeutiques (LR16IPT08), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia;
| | - Monia Ardhaoui
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
- Laboratory of Molecular Epidemiology & Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia
| | - Mouna Safer
- National Observatory of New and Emergent Diseases, Tunis 1002, Tunisia; (M.S.); (N.B.A.)
| | - Nissaf Ben Alaya
- National Observatory of New and Emergent Diseases, Tunis 1002, Tunisia; (M.S.); (N.B.A.)
| | - Ikram Guizani
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
- Laboratory of Molecular Epidemiology & Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1068, Tunisia; (W.K.R.); (R.K.)
| | - Mariem Gdoura
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
| | - Henda Triki
- Reasearch Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health”, LR20IPT02, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (W.F.); (A.L.); (S.H.-B.); (Z.B.); (K.A.); (M.K.); (H.T.); (I.B.D.); (M.G.); (H.T.)
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (S.B.H.); (H.K.)
- Clinical Investigation Center (CIC), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia; (M.A.); (I.G.)
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9
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Basheer A, Zahoor I. Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan. Microorganisms 2021; 9:microorganisms9122609. [PMID: 34946210 DOI: 10.1101/2021.07.28.21261233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 05/28/2023] Open
Abstract
The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.
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Affiliation(s)
- Atia Basheer
- Genetics and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan
| | - Imran Zahoor
- Genetics and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan
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10
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Basheer A, Zahoor I. Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan. Microorganisms 2021; 9:2609. [PMID: 34946210 PMCID: PMC8708969 DOI: 10.3390/microorganisms9122609] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.
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Affiliation(s)
| | - Imran Zahoor
- Genetics and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan;
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11
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Banks JM, Capistrano K, Thakkar P, Ranade H, Soni V, Datta M, Naqvi AR. Current molecular diagnostics assays for SARS-CoV-2 and emerging variants. METHODS IN MICROBIOLOGY 2021; 50:83-121. [PMID: 38620738 PMCID: PMC8655725 DOI: 10.1016/bs.mim.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Since the SARS-CoV-2 virus triggered the beginning of the COVID-19 pandemic, scientists, government officials, and healthcare professionals around the world recognized the need for accessible, affordable, and accurate testing to predict and contain the spread of COVID-19. In the months that followed, research teams designed, tested, and rolled out hundreds of diagnostic assays, each with different sampling methods, diagnostic technologies, and sensitivity levels. However, the contagious virus continued to spread; SARS-CoV-2 travelled through airborne particles and spread rapidly, despite the widening use of diagnostic assays. As the pandemic continued, hundreds of millions of people contracted COVID-19 and millions died worldwide. With so many infections, SARS-CoV-2 received many opportunities to replicate and mutate, and from these mutations emerged more contagious, deadly, and difficult-to-diagnose viral mutants. Each change to the viral genome presented potential added challenges to containing the virus, and as such, researchers have continued developing and improving testing methods to keep up with COVID-19. In this chapter, we examine several SARS-CoV-2 variants that have emerged during the pandemic. Additionally, we discuss a few major COVID-19 diagnostic technique categories, including those involving real-time PCR, serology, CRISPR, and electronic biosensors. Finally, we address SARS-CoV-2 variants and diagnostic assays in the age of COVID-19 vaccines.
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Affiliation(s)
- Jonathan M Banks
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
| | - Kristelle Capistrano
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
| | - Pari Thakkar
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
| | - Hemangi Ranade
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Vaidik Soni
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
| | - Manali Datta
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Afsar R Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, United States
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12
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da Silva Francisco Junior R, Lamarca AP, de Almeida LGP, Cavalcante L, Machado DT, Martins Y, Brustolini O, Gerber AL, de C Guimarães AP, Gonçalves RB, Alves C, Mariani D, Cruz TF, de Souza IV, de Carvalho EM, Ribeiro MS, Carvalho S, da Silva FD, de Oliveira Garcia MH, de Souza LM, da Silva CG, Ribeiro CLP, Cavalcanti AC, de Mello CMB, Struchiner CJ, Tanuri A, Vasconcelos ATR. Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil. Viruses 2021; 13:2013. [PMID: 34696443 PMCID: PMC8537965 DOI: 10.3390/v13102013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023] Open
Abstract
In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion.
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Affiliation(s)
- Ronaldo da Silva Francisco Junior
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Alessandra P Lamarca
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Luiz G P de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Liliane Cavalcante
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Douglas Terra Machado
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Yasmmin Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Otávio Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Alexandra L Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Ana Paula de C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Reinaldo Bellini Gonçalves
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
| | - Cassia Alves
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Diana Mariani
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Thais Felix Cruz
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | | | - Erika Martins de Carvalho
- Unidades de Apoio ao Diagnóstico da COVID-19, Rio de Janeiro 21040-900, Brazil; (I.V.d.S.); (E.M.d.C.)
| | - Mario Sergio Ribeiro
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | - Silvia Carvalho
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | - Flávio Dias da Silva
- Secretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, Brazil; (F.D.d.S.); (M.H.d.O.G.); (C.L.P.R.)
| | | | - Leandro Magalhães de Souza
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Cristiane Gomes da Silva
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Caio Luiz Pereira Ribeiro
- Secretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, Brazil; (F.D.d.S.); (M.H.d.O.G.); (C.L.P.R.)
| | - Andréa Cony Cavalcanti
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, Brazil; (L.M.d.S.); (C.G.d.S.); (A.C.C.)
| | - Claudia Maria Braga de Mello
- Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, Brazil; (M.S.R.); (S.C.); (C.M.B.d.M.)
| | | | - Amilcar Tanuri
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, Brazil; (C.A.); (D.M.); (T.F.C.); (A.T.)
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, Brazil; (R.d.S.F.J.); (A.P.L.); (L.G.P.d.A.); (L.C.); (D.T.M.); (Y.M.); (O.B.); (A.L.G.); (A.P.d.C.G.); (R.B.G.)
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13
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Al-Lawama M, Badran E, Ghanim N, Irsheid A, Qtaishat H, Al-Ammouri I, Al-Zyadneh E, Al-Iede M, Daher AH, Bakri FG, Massad G. Perinatal Transmission and Clinical Outcomes of Neonates Born to SARS-CoV-2-Positive Mothers. J Clin Med Res 2021; 13:420-424. [PMID: 34527097 PMCID: PMC8425792 DOI: 10.14740/jocmr4578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 08/20/2021] [Indexed: 12/25/2022] Open
Abstract
Background The aim of the study was to investigate the clinical outcomes and rate of virus detection in neonates born to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive mothers. Methods This prospective study included neonates born to SARS-CoV-2-positive mothers, documenting their viral polymerase chain reaction results and clinical outcomes. Results Of the 130 neonates born to 122 SARS-CoV-2-positive mothers, 12% tested positive. Most (62%) neonates were delivered via cesarean section at an average gestational age of 36 weeks, with a birth weight of 2,900 g. Only 38% neonates required admission. SARS-CoV-2-positive infants were born at a significantly lower gestational age; had a significantly lower birth weight; and had significantly higher admission rates, surfactant therapy, and bradycardia than SARS-CoV-2-negative infants. There was no significant difference in mortality rates. Conclusion This study documents perinatal transmission of SARS-CoV-2. It reports for the first time the occurrence of neonatal bradycardia as a complication of maternal SARS-CoV-2 infection. Despite that, neonates born to SARS-CoV-2-positive mothers had relatively good short-term outcomes.
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Affiliation(s)
- Manar Al-Lawama
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Eman Badran
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Noor Ghanim
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Ayah Irsheid
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Hiba Qtaishat
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Iyad Al-Ammouri
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Enas Al-Zyadneh
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Montaha Al-Iede
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Amira H Daher
- Pediatric Department, School of Medicine, The University of Jordan, Amman, Jordan
| | - Fares G Bakri
- Division of Infectious Diseases, Department of Medicine, Jordan University Hospital, Amman, Jordan.,Infectious Disease and Vaccine Center, The University of Jordan, Amman, Jordan
| | - Ghada Massad
- Nursing Department, Jordan University Hospital, Amman, Jordan
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14
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Temsah MH, Barry M, Aljamaan F, Alhuzaimi AN, Al-Eyadhy A, Saddik B, Alsohime F, Alhaboob A, Alhasan K, Alaraj A, Halwani R, Jamal A, Alamro N, Temsah R, Esmaeil S, Alenezi S, Alzamil F, Somily AM, Al-Tawfiq JA. SARS-CoV-2 B.1.1.7 UK Variant of Concern Lineage-Related Perceptions, COVID-19 Vaccine Acceptance and Travel Worry Among Healthcare Workers. Front Public Health 2021; 9:686958. [PMID: 34123997 PMCID: PMC8187763 DOI: 10.3389/fpubh.2021.686958] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/28/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Healthcare workers' (HCWs') travel-related anxiety needs to be assessed in light of the emergence of SARS-CoV-2 mutations. Methods: An online, cross-sectional questionnaire among HCWs between December 21, 2020 to January 7, 2021. The outcome variables were HCWs' knowledge and awareness of the SARS-CoV-2 B.1.1.7 lineage that was recently reported as the UK variant of concern, and its associated travel worry and Generalized Anxiety Disorder (GAD-7) score. Results: A total of 1,058 HCWs completed the survey; 66.5% were female, 59.0% were nurses. 9.0% indicated they had been previously diagnosed with COVID-19. Regarding the B.1.1.7 lineage, almost all (97.3%) were aware of its emergence, 73.8% were aware that it is more infectious, 78.0% thought it causes more severe disease, and only 50.0% knew that current COVID-19 vaccines are effective in preventing it. Despite this, 66.7% of HCWs were not registered to receive the vaccine. HCWs' most common source of information about the new variant was social media platforms (67.0%), and this subgroup was significantly more worried about traveling. Nurses were more worried than physicians (P = 0.001). Conclusions: Most HCWs were aware of the emergence of the SARS-CoV-2 B.1.1.7 variant and expressed substantial travel worries. Increased worry levels were found among HCWs who used social media as their main source of information, those with lower levels of COVID-19 vaccine uptake, and those with higher GAD-7 scores. The utilization of official social media platforms could improve accurate information dissemination among HCWs regarding the Pandemic's evolving mutations. Targeted vaccine campaigns are warranted to assure HCWs about the efficacy of COVID-19 vaccines toward SARS-CoV-2 variants.
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Affiliation(s)
- Mohamad-Hani Temsah
- Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mazin Barry
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, King Saud University and King Saud University Medical City, Riyadh, Saudi Arabia
| | - Fadi Aljamaan
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Critical Care Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah N. Alhuzaimi
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Division of Pediatric Cardiology, Department of Cardiac Sciences, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Heart Center, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Ayman Al-Eyadhy
- Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Basema Saddik
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Community and Family Medicine, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Fahad Alsohime
- Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ali Alhaboob
- Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Khalid Alhasan
- Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ali Alaraj
- Dr Sulaiman Al Habib Medical Group, Riyadh, Saudi Arabia
- Department of Medicine, College of Medicine, Qassim University, Qassim, Saudi Arabia
| | - Rabih Halwani
- Sharjah Institute of Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Amr Jamal
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Department of Family and Community Medicine, King Saud University Medical City, Riyadh, Saudi Arabia
- Evidence-Based Health Care & Knowledge Translation Research Chair, King Saud University, Riyadh, Saudi Arabia
| | - Nurah Alamro
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Department of Family and Community Medicine, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Reem Temsah
- College of Pharmacy, Alfaisal University, Riyadh, Saudi Arabia
| | - Samia Esmaeil
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Evidence-Based Health Care & Knowledge Translation Research Chair, King Saud University, Riyadh, Saudi Arabia
| | - Shuliweeh Alenezi
- Department of Psychiatry, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Fahad Alzamil
- Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ali M. Somily
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University and King Saud University Medical City, Riyadh, Saudi Arabia
| | - Jaffar A. Al-Tawfiq
- Specialty Internal Medicine and Quality Department, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- Infectious Disease Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
- Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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