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Suljič A, Zorec TM, Zakotnik S, Vlaj D, Kogoj R, Knap N, Petrovec M, Poljak M, Avšič-Županc T, Korva M. Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing. Brief Bioinform 2024; 25:bbae263. [PMID: 38833323 PMCID: PMC11149657 DOI: 10.1093/bib/bbae263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/23/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024] Open
Abstract
The emergence and rapid spread of SARS-CoV-2 prompted the global community to identify innovative approaches to diagnose infection and sequence the viral genome because at several points in the pandemic positive case numbers exceeded the laboratory capacity to characterize sufficient samples to adequately respond to the spread of emerging variants. From week 10, 2020, to week 13, 2023, Slovenian routine complete genome sequencing (CGS) surveillance network yielded 41 537 complete genomes and revealed a typical molecular epidemiology with early lineages gradually being replaced by Alpha, Delta, and finally Omicron. We developed a targeted next-generation sequencing based variant surveillance strategy dubbed Spike Screen through sample pooling and selective SARS-CoV-2 spike gene amplification in conjunction with CGS of individual cases to increase throughput and cost-effectiveness. Spike Screen identifies variant of concern (VOC) and variant of interest (VOI) signature mutations, analyses their frequencies in sample pools, and calculates the number of VOCs/VOIs at the population level. The strategy was successfully applied for detection of specific VOC/VOI mutations prior to their confirmation by CGS. Spike Screen complemented CGS efforts with an additional 22 897 samples sequenced in two time periods: between week 42, 2020, and week 24, 2021, and between week 37, 2021, and week 2, 2022. The results showed that Spike Screen can be applied to monitor VOC/VOI mutations among large volumes of samples in settings with limited sequencing capacity through reliable and rapid detection of novel variants at the population level and can serve as a basis for public health policy planning.
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Affiliation(s)
- Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Tomaž Mark Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Samo Zakotnik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Doroteja Vlaj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, 1000 Ljubljana, Slovenia
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Rabaan AA, Bello KE, Irekeola AA, Kaabi NAA, Halwani MA, Yousuf AA, Alshengeti A, Alfaraj AH, Khamis F, Al-Subaie MF, AlShehail BM, Almuthree SA, Ibraheem NY, Khalifa MH, Alfaresi M, Fares MAA, Garout M, Alsayyah A, Alshehri AA, Alqahtani AS, Alissa M. Prevalence of Hepatocellular Carcinoma in Hepatitis B Population within Southeast Asia: A Systematic Review and Meta-Analysis of 39,050 Participants. Pathogens 2023; 12:1220. [PMID: 37887736 PMCID: PMC10609743 DOI: 10.3390/pathogens12101220] [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: 08/17/2023] [Revised: 09/09/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND AND AIM Hepatocellular carcinoma (HCC) is a significant complication of hepatitis B and still poses a global public health concern. This systematic review and meta-analysis provide adequate details on the prevalence of HCC in the HBV population within Southeast Asian countries. METHOD Following the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) criteria, a thorough search for literature discussing the prevalence of HCC in the HBV population within southeast Asia was performed. Eligible studies were subjected to a meta-analysis utilising a DerSimonian and Laird approach and a random effect model. A protocol was registered with PROSPERO (CRD42023423953). RESULT Our study meticulously recovered 41 articles from seven countries in Southeast Asia, namely Cambodia, Indonesia, Malaysia, the Philippines, Singapore, Thailand, and Vietnam. A total of 39,050 HBV patients and 7479 HCC cases in southeast Asia were analysed. The pooled prevalence of HCC in HBV cases within southeast Asia was 45.8% (95% CI, 34.3-57.8%, I2 = 99.51%, p < 0.001). Singapore (62.5%, CI: 42.4-79.1) had the highest pooled prevalence of HCC in the HBV population compared to Vietnam, with the lowest estimate (22.4%, CI: 9.9-44.9). There was a drop in the pooled prevalence of HCC in HBV from 2016 until now (37.6%, CI: 19.2-60.5). CONCLUSION The findings of this review reveal a high pooled prevalence of HCC in the HBV population and therefore stir the need for routine screening, management, and surveillance.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Kizito Eneye Bello
- Department of Microbiology, Faculty of Natural Science, Kogi State University (Prince Abubakar Audu University) Anyigba, Anyigba PMB 1008, Nigeria
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, Offa PMB 4412, Nigeria
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Muhammad A. Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha 4781, Saudi Arabia
| | - Amjad A. Yousuf
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Amal H. Alfaraj
- Pediatric Department, Abqaiq General Hospital, First Eastern Health Cluster, Abqaiq 33261, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases Unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Maha F. Al-Subaie
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Research Center, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia
- Department of Infectious Diseases, Dr. Sulaiman Alhabib Medical Group, Riyadh 13328, Saudi Arabia
| | - Bashayer M. AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Souad A. Almuthree
- Department of Infectious Disease, King Abdullah Medical City, Makkah 43442, Saudi Arabia
| | - Noha Y. Ibraheem
- Department of Infectious Disease, King Abdullah Medical City, Makkah 43442, Saudi Arabia
| | - Mahassen H. Khalifa
- Department of Infectious Disease, King Abdullah Medical City, Makkah 43442, Saudi Arabia
| | - Mubarak Alfaresi
- Department of Pathology and Laboratory Medicine, Zayed Military Hospital, Abu Dhabi 3740, United Arab Emirates
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ahmed Alsayyah
- Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ali S. Alqahtani
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Khalid University, Abha 61481, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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Perveen I, Bukhari B, Najeeb M, Nazir S, Faridi TA, Farooq M, Ahmad QUA, Abusalah MAHA, ALjaraedah TY, Alraei WY, Rabaan AA, Singh KKB, Abusalah MAHA. Hydrogen Therapy and Its Future Prospects for Ameliorating COVID-19: Clinical Applications, Efficacy, and Modality. Biomedicines 2023; 11:1892. [PMID: 37509530 PMCID: PMC10377251 DOI: 10.3390/biomedicines11071892] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 07/30/2023] Open
Abstract
Molecular hydrogen is renowned as an odorless and colorless gas. The recommendations developed by China suggest that the inhalation of hydrogen molecules is currently advised in COVID-19 pneumonia treatment. The therapeutic effects of molecular hydrogens have been confirmed after numerous clinical trials and animal-model-based experiments, which have expounded that the low molecular weight of hydrogen enables it to easily diffuse and permeate through the cell membranes to produce a variety of biological impacts. A wide range of both chronic and acute inflammatory diseases, which may include sepsis, pancreatitis, respiratory disorders, autoimmune diseases, ischemia-reperfusion damages, etc. may be treated and prevented by using it. H2 can primarily be inoculated through inhalation, by drinking water (which already contains H2), or by administrating the injection of saline H2 in the body. It may play a pivotal role as an antioxidant, in regulating the immune system, in anti-inflammatory activities (mitochondrial energy metabolism), and cell death (apoptosis, pyroptosis, and autophagy) by reducing the formation of excessive reactive O2 species and modifying the transcription factors in the nuclei of the cells. However, the fundamental process of molecular hydrogen is still not entirely understood. Molecular hydrogen H2 has a promising future in therapeutics based on its safety and possible usefulness. The current review emphasizes the antioxidative, anti-apoptotic, and anti-inflammatory effects of hydrogen molecules along with the underlying principle and fundamental mechanism involved, with a prime focus on the coronavirus disease of 2019 (COVID-19). This review will also provide strategies and recommendations for the therapeutic and medicinal applications of the hydrogen molecule.
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Affiliation(s)
- Ishrat Perveen
- Food and Biotechnology Research Centre, Pakistan Council of Scientific and Industrial Research Centre, Lahore 54590, Pakistan
| | - Bakhtawar Bukhari
- Food and Biotechnology Research Centre, Pakistan Council of Scientific and Industrial Research Centre, Lahore 54590, Pakistan
| | - Mahwish Najeeb
- University Institute of Public Health, The University of Lahore, Lahore 54590, Pakistan
| | - Sumbal Nazir
- School of Zoology, Minhaj University Lahore, Lahore 54770, Pakistan
| | - Tallat Anwar Faridi
- University Institute of Public Health, The University of Lahore, Lahore 54590, Pakistan
| | - Muhammad Farooq
- Food and Biotechnology Research Centre, Pakistan Council of Scientific and Industrial Research Centre, Lahore 54590, Pakistan
| | - Qurat-Ul-Ain Ahmad
- Division of Science and Technology, University of Education, Township Lahore, Lahore 54770, Pakistan
| | - Manal Abdel Haleem A Abusalah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Thana' Y ALjaraedah
- Department of Diet Therapy Technology & Dietetics, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
| | - Wesal Yousef Alraei
- Department of Diet Therapy Technology & Dietetics, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Mai Abdel Haleem A Abusalah
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Zarqa University, Al-Zarqa 13132, Jordan
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Marascio N, Cilburunoglu M, Torun EG, Centofanti F, Mataj E, Equestre M, Bruni R, Quirino A, Matera G, Ciccaglione AR, Yalcinkaya KT. Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month. Viruses 2023; 15:v15030802. [PMID: 36992510 PMCID: PMC10054778 DOI: 10.3390/v15030802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
The SARS-CoV-2 pandemic has seriously affected the population in Turkey. Since the beginning, phylogenetic analysis has been necessary to monitor public health measures against COVID-19 disease. In any case, the analysis of spike (S) and nucleocapsid (N) gene mutations was crucial in determining their potential impact on viral spread. We screened S and N regions to detect usual and unusual substitutions, whilst also investigating the clusters among a patient cohort resident in Kahramanmaraş city, in a restricted time span. Sequences were obtained by Sanger methods and genotyped by the PANGO Lineage tool. Amino acid substitutions were annotated comparing newly generated sequences to the NC_045512.2 reference sequence. Clusters were defined using phylogenetic analysis with a 70% cut-off. All sequences were classified as Delta. Eight isolates carried unusual mutations on the S protein, some of them located in the S2 key domain. One isolate displayed the unusual L139S on the N protein, while few isolates carried the T24I and A359S N substitutions able to destabilize the protein. Phylogeny identified nine monophyletic clusters. This study provided additional information about SARS-CoV-2 epidemiology in Turkey, suggesting local transmission of infection in the city by several transmission routes, and highlighting the necessity to improve the power of sequencing worldwide.
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Affiliation(s)
- Nadia Marascio
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | - Merve Cilburunoglu
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
| | - Elif Gulsum Torun
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
| | - Federica Centofanti
- Department of Applied Clinical Sciences and Biotechnology, University of Aquila, 67100 L'Aquila, Italy
| | - Elida Mataj
- Instituti i Shendetit Publik (ISHP), 1000 Tirana, Albania
| | - Michele Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Angela Quirino
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | - Giovanni Matera
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | | | - Kezban Tulay Yalcinkaya
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
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AL-Mhanna SB, Wan Ghazali WS, Mohamed M, Sheikh AM, Tabnjh AK, Afolabi H, Mutalub YB, Adeoye AO, Mohamed Nur M, Aldhahi MI. Evaluation of physical activity among undergraduate students in Mogadishu Universities in the aftermath of COVID-19 restrictions. PeerJ 2022; 10:e14131. [PMID: 36248716 PMCID: PMC9558621 DOI: 10.7717/peerj.14131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/06/2022] [Indexed: 01/21/2023] Open
Abstract
Background International restrictions were enacted during the COVID-19 pandemic to limit social interaction and viral transmission. These measures had a negative impact on physical activity (PA), creating changes in students' health and lifestyles. The present study aimed to evaluate the levels of PA among undergraduate students in three different universities in Mogadishu after the relaxation of COVID-19 lockdown using the international physical activity questionnaire-long version (IPAQ-L) and its potential associated factors. Methods This study is a multicentral study conducted at Somali International University, Horn of Africa University, and Daha International University. A total of 1,189 respondents were asked to answer the online questionnaire provided via a link shared using their social media. Results After COVID-19 restrictions approximately ≥ 150 minutes of PA per week was reported by 500 men (97.3%) and 652 women (96.6%) at work. While 7 (1.4%) of men and 20 (3%) of women participate in < 150 minutes each week, respectively. Furthermore, only seven (1.4%) of males and three (0.4%) of women reported to have not performed any PA at work. Conclusion The majority of the undergraduate students at the selected universities in Mogadishu were physically active after the relaxation of COVID-19 rules in Somalia. Such a high level of PA is a significant advantage to public health.
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Affiliation(s)
- Sameer Badri AL-Mhanna
- Department of Physiology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Wan Syaheedah Wan Ghazali
- Department of Physiology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Mahaneem Mohamed
- Department of Physiology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | | | | | - HafeezAbiola Afolabi
- Department of General Surgery, Universiti Sains Malaysia, Kota bharu, Kelantan, Malaysia
| | - Yahkub Babatunde Mutalub
- Department of Clinical Pharmacology, College of Medical Sciences, Abubakar Tafawa Balewa University, Bauchi, Bauchi, Nigeria
| | - Azeez Omoniyi Adeoye
- Anatomy Department, Kampala International University, Bushenyi-Uganda, Bushenyi, Uganda
| | - Mariam Mohamed Nur
- Faculty of Health Science, Somali International University, Mogadishu, Somalia
| | - Monira I. Aldhahi
- Department of Rehabilitation Sciences, College of Health and Rehabilitation Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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Gaiarsa S, Giardina F, Batisti Biffignandi G, Ferrari G, Piazza A, Tallarita M, Novazzi F, Bandi C, Paolucci S, Rovida F, Campanini G, Piralla A, Baldanti F. Comparative analysis of SARS-CoV-2 quasispecies in the upper and lower respiratory tract shows an ongoing evolution in the spike cleavage site. Virus Res 2022; 315:198786. [PMID: 35429618 PMCID: PMC9008095 DOI: 10.1016/j.virusres.2022.198786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/14/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023]
Abstract
Studies are needed to better understand the genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe viral quasispecies population of upper and lower respiratory tract by next-generation sequencing in patients admitted to intensive care unit. A deep sequencing of the S gene of SARS-CoV-2 from 109 clinical specimens, sampled from the upper respiratory tract (URT) and lower respiratory tract (LRT) of 77 patients was performed. A higher incidence of non-synonymous mutations and indels was observed in the LRT among minority variants. This might be explained by the ability of the virus to invade cells without interacting with ACE2 (e.g. exploiting macrophage phagocytosis). Minority variants are highly concentrated around the gene portion encoding for the Spike cleavage site, with a higher incidence in the URT; four mutations are highly recurring among samples and were found associated with the URT. Interestingly, 55.8% of minority variants detected in this locus were T>G and G>T transversions. Results from this study evidenced the presence of selective pressure and suggest that an evolutionary process is still ongoing in one of the crucial sites of spike protein associated with the spillover to humans.
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Affiliation(s)
- Stefano Gaiarsa
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Federica Giardina
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | | | - Guglielmo Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Aurora Piazza
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Monica Tallarita
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Federica Novazzi
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Claudio Bandi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Stefania Paolucci
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Francesca Rovida
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Giulia Campanini
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy.
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Via Tamelli 5, Pavia 27100, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
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Vasan PK, Shinde O, Banga KS, Basha S, Karobari MI, Basheer SN, Mirza MB, Pawar AM. COVID-19 Contraction Among Dental Healthcare Workers in the Department of Conservative Dentistry and Endodontics - A Retrospective Analysis During the Pandemic. Healthc Policy 2022; 15:1243-1252. [PMID: 35769498 PMCID: PMC9234192 DOI: 10.2147/rmhp.s368076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/04/2022] [Indexed: 12/01/2022] Open
Abstract
Introduction The COVID-19 pandemic has led to major challenges for the healthcare sector across the globe including dental healthcare workers (DHCWs) due to the increased risk of transmission of virus during aerosol-generating procedures. We conducted the present retrospective analysis determining the risk of contraction of COVID-19 infection among DHCWs since the outbreak of the pandemic for a year (March 2020 through March 2021) in Mumbai. Methods In total, 18,058 patients visited the Nair Hospital Dental College for dental treatment related to the Department of Conservative Dentistry and Endodontics during the assessed year. All the patients were subjected to intensive triage, which included recording their body temperature, oxygen saturation level, travel, and COVID-19 exposure history. Results A total of 26 DHCWs were responsible for attending and treating the patients with all the standard infection control measures. Seventy-four (0.40%) patients out of 18058 were referred for a nasal rapid antigen test (RAT) on giving a positive affirmation about COVID-19 like symptoms when screened at the triage. Of those 74 patients referred, 20 reported a positive nasal rapid antigen test and the infection was confirmed by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR). Among 26, 9 (34,7%) DCHWs were found to have contracted the infection during the assessed year. Conclusion The analysis found that the risk of COVID-19 infection contraction amongst the DHCWs is considerably less. This could be attributed to the intensive triage and the preventive measures taken while rendering treatment.
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Affiliation(s)
- Purveet Kaur Vasan
- Department of Conservative Dentistry and Endodontics, Nair Hospital Dental College, Mumbai, Maharashtra, 400008, India
| | - Omkar Shinde
- Department of Conservative Dentistry and Endodontics, Nair Hospital Dental College, Mumbai, Maharashtra, 400008, India
| | - Kulvinder Singh Banga
- Department of Conservative Dentistry and Endodontics, Nair Hospital Dental College, Mumbai, Maharashtra, 400008, India
| | - Sakeenabi Basha
- Department of Community Dentistry, Faculty of Dentistry, Taif University, Taif, 21944, Saudi Arabia
| | - Mohmed Isaqali Karobari
- Department of Restorative Dentistry & Endodontics, Faculty of Dentistry, University of Puthisastra, Phnom Penh, 12211, Cambodia.,Conservative Dentistry & Endodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences University, Chennai, Tamil Nadu, 600077, India
| | - Syed Nahid Basheer
- Department of Restorative Dental Sciences, College of Dentistry, Jazan University, Jazan, 45142, Kingdom of Saudi Arabia
| | - Mubashir Baig Mirza
- Conservative Dental Science Department, College of Dentistry, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Kingdom of Saudi Arabia
| | - Ajinkya M Pawar
- Department of Conservative Dentistry and Endodontics, Nair Hospital Dental College, Mumbai, Maharashtra, 400008, India
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Ubiquitous Micro-Modular Homologies among Genomes from Viruses to Bacteria to Human Mitochondrial DNA: Platforms for Recombination during Evolution? Viruses 2022; 14:v14050885. [PMID: 35632627 PMCID: PMC9147251 DOI: 10.3390/v14050885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/16/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022] Open
Abstract
The emerging Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and its variants have raised tantalizing questions about evolutionary mechanisms that continue to shape biology today. We have compared the nucleotide sequence of SARS-CoV-2 RNA to that of genomes of many different viruses, of endosymbiotic proteobacterial and bacterial DNAs, and of human mitochondrial DNA. The entire 4,641,652 nt DNA sequence of Escherichia coli K12 has been computer-matched to SARS-CoV-2 RNA. Numerous, very similar micro-modular clusters of 3 to 13 nucleotides lengths were detected with sequence identities of 40 to >50% in specific genome segments between SARS-CoV-2 and the investigated genomes. These clusters were part of patch-type homologies. Control sequence comparisons between 1000 randomly computer-composed sequences of 29.9 kb and with the A, C, G, T base composition of SARS-CoV-2 genome versus the reference Wuhan SARS-CoV-2 sequence showed similar patterns of sequence homologies. The universal A, C, G, T genetic coding mode might have succeeded in evolution due in part to its built-in capacity to select for a substantial reservoir of micro-modular domains and employ them as platforms for integrative recombination. Their role in SARS-CoV-2 interspecies transition and the generation of variants appears likely, but their actual involvement will require detailed investigations.
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Evaluation of Bi-Lateral Co-Infections and Antibiotic Resistance Rates among COVID-19 Patients. Antibiotics (Basel) 2022; 11:antibiotics11020276. [PMID: 35203877 PMCID: PMC8868529 DOI: 10.3390/antibiotics11020276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
In addition to the pathogenesis of SARS-CoV-2, bacterial co-infection plays an essential role in the incidence and progression of SARS-CoV-2 infections by increasing the severity of infection, as well as increasing disease symptoms, death rate and antimicrobial resistance (AMR). The current study was conducted in a tertiary-care hospital in Lahore, Pakistan, among hospitalized COVID-19 patients to see the prevalence of bacterial co-infections and the AMR rates among different isolated bacteria. Clinical samples for the laboratory diagnosis were collected from 1165 hospitalized COVID-19 patients, of which 423 were found to be positive for various bacterial infections. Most of the isolated bacteria were Gram-negative rods (n = 366), followed by Gram-positive cocci (n = 57). A significant association (p < 0.05) was noted between the hospitalized COVID-19 patients and bacterial co-infections. Staphylococcus aureus (S. aureus) showed high resistance against tetracycline (61.7%), Streptococcus pyogenes against penicillin (100%), E. coli against Amp-clavulanic acid (88.72%), Klebsiella pneumoniae against ampicillin (100%), and Pseudomonas aeruginosa against ciprofloxacin (75.40%). Acinetobacter baumannii was 100% resistant to the majority of tested antibiotics. The prevalence of methicillin-resistant S. aureus (MRSA) was 14.7%. The topmost symptoms of >50% of COVID-19 patients were fever, fatigue, dyspnea and chest pain with a significant association (p < 0.05) in bacterial co-infected patients. The current study results showed a comparatively high prevalence of AMR, which may become a severe health-related issue in the future. Therefore, strict compliance of antibiotic usage and employment of antibiotic stewardship programs at every public or private institutional level are recommended.
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Parra-Lucares A, Segura P, Rojas V, Pumarino C, Saint-Pierre G, Toro L. Emergence of SARS-CoV-2 Variants in the World: How Could This Happen? Life (Basel) 2022; 12:194. [PMID: 35207482 PMCID: PMC8879166 DOI: 10.3390/life12020194] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has had a significant global impact, with more than 280,000,000 people infected and 5,400,000 deaths. The use of personal protective equipment and the anti-SARS-CoV-2 vaccination campaigns have reduced infection and death rates worldwide. However, a recent increase in infection rates has been observed associated with the appearance of SARS-CoV-2 variants, including the more recently described lineage B.1.617.2 (Delta variant) and lineage B.1.1.529/BA.1 (Omicron variant). These new variants put the effectiveness of international vaccination at risk, with the appearance of new outbreaks of COVID-19 throughout the world. This emergence of new variants has been due to multiple predisposing factors, including molecular characteristics of the virus, geographic and environmental conditions, and the impact of social determinants of health that favor the genetic diversification of SARS-CoV-2. We present a literature review on the most recent information available on the emergence of new variants of SARS-CoV-2 in the world. We analyzed the biological, geographical, and sociocultural factors that favor the development of these variants. Finally, we evaluate the surveillance strategies for the early detection of new variants and prevent their distribution outside these regions.
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Affiliation(s)
- Alfredo Parra-Lucares
- Division of Critical Care Medicine, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile; (A.P.-L.); (V.R.)
| | - Paula Segura
- Department of Anatomic Pathology, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile;
| | - Verónica Rojas
- Division of Critical Care Medicine, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile; (A.P.-L.); (V.R.)
- Centro de Investigación Clínica Avanzada, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
| | - Catalina Pumarino
- School of Medicine, Faculty of Medicine, Universidad de Chile, 8380456 Santiago, Chile;
| | - Gustavo Saint-Pierre
- Microbiology Unit, Clinical Laboratory, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile;
| | - Luis Toro
- Centro de Investigación Clínica Avanzada, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
- Division of Nephrology, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
- Critical Care Unit, Clínica Las Condes, 7591047 Santiago, Chile
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