1
|
Menezes RC, Ferreira IBB, Sobral L, Garcia SL, Pustilnik HN, Araújo-Pereira M, Andrade BB. Severe viral lower respiratory tract infections in Brazilian children: Clinical features of a national cohort. J Infect Public Health 2024; 17:1-9. [PMID: 37988811 DOI: 10.1016/j.jiph.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/28/2023] [Accepted: 09/25/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND The accurate etiological diagnosis of lower respiratory tract infections (LRTI) is essential for their effective clinical management. The extensive use of molecular methods during the COVID-19 pandemic has enabled massive data acquisition on viral lower respiratory tract infections. The current study aims to identify clinical features associated with eight viral agents among children presenting severe LRTI. METHODS retrospective cohort study of data from the Brazilian Influenza Epidemiological Surveillance Information System. Patients under 20 years-old who had severe LRTI with etiological confirmation through RT-PCR between 2020 and 2022 were included. Binary logistic regressions were used to examine associations between pathogens and symptoms. RESULTS 60,657 cases were assessed. The main viral agents detected were Sars-CoV-2 (COV2) (41.2%), Respiratory Syncytial Virus (29.1%), Human Rhinovirus (HRV) (12.1%), and Influenza (FLU) (5.5%). A general mortality rate of 4.3% was observed. The multivariate analysis evidenced that COV2 less likely presented with cough (OR: 0.34; 95%CI: 0.32-0.36), respiratory discomfort (Adjusted Odds Ratio (aOR): 0.61; 95%Confidence Interval (CI): 0.59-0.64), and desaturation (aOR: 0.71; 95%CI: 0.69-0.75). RSV strongly associated with cough (aOR: 2.59; 95%CI: 2.45-2.75) and respiratory discomfort (aOR: 1.54; 95%CI: 1.46-1.62), whereas FLU was linked to fever (aOR: 2.27; 95%CI: 2.06-2.50) and sore throat (aOR: 1.48; 95%CI: 1.34-1.64). CONCLUSIONS The viral agents responsible for severe LRTI have distinct associations with clinical features in children.
Collapse
Affiliation(s)
- Rodrigo C Menezes
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER Initiative), Brazil; Instituto de Pesquisa Clínica e Translacional (IPCT), UniFTC, Bahia, Brazil; Universidade Federal da Bahia (UFBA), Bahia, Brazil; Fundação Oswaldo Cruz (FIOCRUZ), Bahia, Brazil
| | - Isabella B B Ferreira
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER Initiative), Brazil; Instituto de Pesquisa Clínica e Translacional (IPCT), UniFTC, Bahia, Brazil; Escola Bahiana de Medicina e Saúde Pública (EBMSP), Bahia, Brazil
| | - Luciana Sobral
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER Initiative), Brazil; Instituto de Pesquisa Clínica e Translacional (IPCT), UniFTC, Bahia, Brazil; Escola Bahiana de Medicina e Saúde Pública (EBMSP), Bahia, Brazil
| | - Stefania L Garcia
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER Initiative), Brazil; Universidade Salvador, Bahia, Brazil
| | - Hugo N Pustilnik
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER Initiative), Brazil; Universidade Salvador, Bahia, Brazil
| | - Mariana Araújo-Pereira
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER Initiative), Brazil; Instituto de Pesquisa Clínica e Translacional (IPCT), UniFTC, Bahia, Brazil; Universidade Federal da Bahia (UFBA), Bahia, Brazil; Fundação Oswaldo Cruz (FIOCRUZ), Bahia, Brazil
| | - Bruno B Andrade
- Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER Initiative), Brazil; Instituto de Pesquisa Clínica e Translacional (IPCT), UniFTC, Bahia, Brazil; Universidade Federal da Bahia (UFBA), Bahia, Brazil; Fundação Oswaldo Cruz (FIOCRUZ), Bahia, Brazil; Universidade Salvador, Bahia, Brazil.
| |
Collapse
|
2
|
Moreira-Soto A, Bruno A, de Mora D, Paez M, Garces J, Wulf B, Sander AL, Olmedo M, Basantes Mantilla MJ, Gonzalez Gonzalez M, Orlando SA, Salgado Cisneros S, Zevallos JC, Drexler JF. Virological evidence of the impact of non-pharmaceutical interventions against COVID-19 in Ecuador, a resource-limited setting. Emerg Microbes Infect 2023; 12:2259001. [PMID: 37698611 PMCID: PMC10563623 DOI: 10.1080/22221751.2023.2259001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/10/2023] [Indexed: 09/13/2023]
Abstract
Ecuador had substantial COVID-19-mortality during 2020 despite early implementation of non-pharmaceutical interventions (NPIs). Resource-limited settings like Ecuador have high proportions of informal labour which entail high human mobility, questioning efficacy of NPIs. We performed a retrospective observational study in Ecuador's national reference laboratory for viral respiratory infections during March 2020-February 2021 using stored respiratory specimens from 1950 patients, corresponding to 2.3% of all samples analysed within the Ecuadorian national surveillance system per week. During 2020, detection of SARS-CoV-2 (Pearson correlation; r = -0.74; p = 0.01) and other respiratory viruses (Pearson correlation; r = -0.68; p = 0.02) by real-time RT-PCR correlated negatively with NPIs stringency. Among respiratory viruses, adenoviruses (Fisher's exact-test; p = 0.026), parainfluenzaviruses (p = 0.04), enteroviruses (p < 0.0001) and metapneumoviruses (p < 0.0001) occurred significantly more frequently during months of absent or non-stringent NPIs (characterized by <55% stringency according to the Oxford stringency index data for Ecuador). Phylogenomic analyses of 632 newly characterized SARS-CoV-2 genomes revealed 100 near-parallel SARS-CoV-2 introductions during early 2020 in the absence of NPIs. NPI stringency correlated negatively with the number of circulating SARS-CoV-2 lineages during 2020 (r = -0.69; p = 0.02). Phylogeographic reconstructions showed differential SARS-CoV-2 dispersion patterns during 2020, with more short-distance transitions potentially associated with recreational activity during non-stringent NPIs. There were also fewer geographic transitions during strict NPIs (n = 450) than during non-stringent or absent NPIs (n = 580). Virological evidence supports that NPIs had an effect on virus spread and distribution in Ecuador, providing a template for future epidemics in resource-limited settings and contributing to a balanced assessment of societal costs entailed by strict NPIs.
Collapse
Affiliation(s)
- Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
- Tropical Disease Research Program, School of Veterinary Medicine, Universidad Nacional, Costa Rica, Costa Rica
| | - Alfredo Bruno
- National Institute of Public Health Research (INSPI), Guayaquil, Ecuador
- Universidad Agraria del Ecuador, Guayaquil, Ecuador
| | - Doménica de Mora
- National Institute of Public Health Research (INSPI), Guayaquil, Ecuador
| | - Michelle Paez
- National Institute of Public Health Research (INSPI), Guayaquil, Ecuador
| | - Jimmy Garces
- National Institute of Public Health Research (INSPI), Guayaquil, Ecuador
| | - Ben Wulf
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Maritza Olmedo
- National Institute of Public Health Research (INSPI), Guayaquil, Ecuador
| | | | - Manuel Gonzalez Gonzalez
- National Institute of Public Health Research (INSPI), Guayaquil, Ecuador
- Universidad ECOTEC, Km 13.5 Samborondon, Samborondon, EC092302, Ecuador
| | - Solon Alberto Orlando
- National Institute of Public Health Research (INSPI), Guayaquil, Ecuador
- Health Science Faculty, Universidad Espíritu Santo, Guayaquil, Ecuador
| | | | - Juan Carlos Zevallos
- Health Science Faculty, Universidad Espíritu Santo, Guayaquil, Ecuador
- Alianza para la Investigación de Enfermedades Emergentes (AIE), Quito, Ecuador
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), Associated Partner Site Charité, Berlin, Germany
| |
Collapse
|
3
|
Frutos AM, Balmaseda A, Vydiswaran N, Patel M, Ojeda S, Brouwer A, Tutino R, Cai S, Bakker K, Sanchez N, Lopez R, Kuan G, Gordon A. Burden and seasonality of primary and secondary symptomatic common cold coronavirus infections in Nicaraguan children. Influenza Other Respir Viruses 2023; 17:e13078. [PMID: 36494188 PMCID: PMC9835451 DOI: 10.1111/irv.13086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The current SARS-CoV-2 pandemic highlights the need for an increased understanding of coronavirus epidemiology. In a pediatric cohort in Nicaragua, we evaluate the seasonality and burden of common cold coronavirus (ccCoV) infection and evaluate likelihood of symptoms in reinfections. METHODS Children presenting with symptoms of respiratory illness were tested for each of the four ccCoVs (NL63, 229E, OC43, and HKU1). Annual blood samples collected before ccCoV infection were tested for antibodies against each ccCoV. Seasonality was evaluated using wavelet and generalized additive model (GAM) analyses, and age-period effects were investigated using a Poisson model. We also evaluate the risk of symptom presentation between primary and secondary infections. RESULTS In our cohort of 2576 children from 2011 to 2016, we observed 595 ccCoV infections and 107 cases of ccCoV-associated lower respiratory infection (LRI). The overall incidence rate was 61.1 per 1000 person years (95% confidence interval (CI): 56.3, 66.2). Children under two had the highest incidence of ccCoV infections and associated LRI. ccCoV incidence rapidly decreases until about age 6. Each ccCoV circulated throughout the year and demonstrated annual periodicity. Peaks of NL63 typically occurred 3 months before 229E peaks and 6 months after OC43 peaks. Approximately 69% of symptomatic ccCoV infections were secondary infections. There was slightly lower risk (rate ratio (RR): 0.90, 95% CI: 0.83, 0.97) of LRI between secondary and primary ccCoV infections among participants under the age of 5. CONCLUSIONS ccCoV spreads annually among children with the greatest burden among ages 0-1. Reinfection is common; prior infection is associated with slight protection against LRI among the youngest children.
Collapse
Affiliation(s)
- Aaron M. Frutos
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Angel Balmaseda
- Health Center Sócrates Flores VivasMinistry of HealthManaguaNicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnósticoy ReferenciaMinistry of HealthManaguaNicaragua
| | - Nivea Vydiswaran
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Mayuri Patel
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | | | - Andrew Brouwer
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Rebecca Tutino
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Shuwei Cai
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Kevin Bakker
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | | | - Roger Lopez
- Laboratorio Nacional de Virología, Centro Nacional de Diagnósticoy ReferenciaMinistry of HealthManaguaNicaragua
- Sustainable Sciences InstituteManaguaNicaragua
| | - Guillermina Kuan
- Health Center Sócrates Flores VivasMinistry of HealthManaguaNicaragua
- Sustainable Sciences InstituteManaguaNicaragua
| | - Aubree Gordon
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| |
Collapse
|
4
|
Cardiovascular Complications of Viral Respiratory Infections and COVID-19. Biomedicines 2022; 11:biomedicines11010071. [PMID: 36672579 PMCID: PMC9856218 DOI: 10.3390/biomedicines11010071] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022] Open
Abstract
Viral respiratory infections (VRI) are the most prevalent type of infectious diseases and constitute one of the most common causes of contact with medical care. Regarding the pathophysiology of the cardiovascular system, VRI can not only exacerbate already existing chronic cardiovascular disease (such as coronary artery disease or heart failure) but also trigger new adverse events or complications (e.g., venous thromboembolism), the latter particularly in subjects with multimorbidity or disease-related immobilization. In the current paper, we provide a narrative review of diverse cardiovascular complications of VRI as well as summarize available data on the pathology of the circulatory system in the course of coronavirus disease 2019 (COVID-19).
Collapse
|
5
|
Balasubramani K, Prasad KA, Kodali NK, Abdul Rasheed NK, Chellappan S, Sarma DK, Kumar M, Dixit R, James MM, Behera SK, Shekhar S, Balabaskaran Nina P. Spatial epidemiology of acute respiratory infections in children under 5 years and associated risk factors in India: District-level analysis of health, household, and environmental datasets. Front Public Health 2022; 10:906248. [PMID: 36582369 PMCID: PMC9792853 DOI: 10.3389/fpubh.2022.906248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/07/2022] [Indexed: 12/15/2022] Open
Abstract
Background In India, acute respiratory infections (ARIs) are a leading cause of mortality in children under 5 years. Mapping the hotspots of ARIs and the associated risk factors can help understand their association at the district level across India. Methods Data on ARIs in children under 5 years and household variables (unclean fuel, improved sanitation, mean maternal BMI, mean household size, mean number of children, median months of breastfeeding the children, percentage of poor households, diarrhea in children, low birth weight, tobacco use, and immunization status of children) were obtained from the National Family Health Survey-4. Surface and ground-monitored PM2.5 and PM10 datasets were collected from the Global Estimates and National Ambient Air Quality Monitoring Programme. Population density and illiteracy data were extracted from the Census of India. The geographic information system was used for mapping, and ARI hotspots were identified using the Getis-Ord Gi* spatial statistic. The quasi-Poisson regression model was used to estimate the association between ARI and household, children, maternal, environmental, and demographic factors. Results Acute respiratory infections hotspots were predominantly seen in the north Indian states/UTs of Uttar Pradesh, Bihar, Delhi, Haryana, Punjab, and Chandigarh, and also in the border districts of Uttarakhand, Himachal Pradesh, and Jammu and Kashmir. There is a substantial overlap among PM2.5, PM10, population density, tobacco smoking, and unclean fuel use with hotspots of ARI. The quasi-Poisson regression analysis showed that PM2.5, illiteracy levels, diarrhea in children, and maternal body mass index were associated with ARI. Conclusion To decrease ARI in children, urgent interventions are required to reduce the levels of PM2.5 and PM10 (major environmental pollutants) in the hotspot districts. Furthermore, improving sanitation, literacy levels, using clean cooking fuel, and curbing indoor smoking may minimize the risk of ARI in children.
Collapse
Affiliation(s)
| | - Kumar Arun Prasad
- Department of Geography, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Naveen Kumar Kodali
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | | | - Savitha Chellappan
- Department of Public Health and Community Medicine, ICMR—National Institute of Traditional Medicine, Belgaum, Karnataka, India
| | - Devojit Kumar Sarma
- Department of Molecular Biology, ICMR—National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Manoj Kumar
- Department of Microbiology, ICMR—National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Rashi Dixit
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Meenu Mariya James
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Sujit Kumar Behera
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Sulochana Shekhar
- Department of Geography, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Praveen Balabaskaran Nina
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India,Department of Public Health and Community Medicine, Central University of Kerala, Kasaragod, Kerala, India,*Correspondence: Praveen Balabaskaran Nina
| |
Collapse
|
6
|
Alonso‐Palomares LA, Cáceres CJ, Tapia R, Aguilera‐Cortés P, Valenzuela S, Valiente‐Echeverría F, Soto‐Rifo R, Gaggero A, Barriga GP. Surveillance of seasonal respiratory viruses among Chilean patients during the COVID-19 pandemic. Health Sci Rep 2021; 4:e433. [PMID: 34849406 PMCID: PMC8611180 DOI: 10.1002/hsr2.433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 11/10/2022] Open
Affiliation(s)
- Luis A. Alonso‐Palomares
- SARS‐CoV‐2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- HIV/AIDS Work Group, Faculty of MedicineUniversidad de ChileSantiagoChile
| | - C. Joaquín Cáceres
- Department of Population Health, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA
| | - Rodrigo Tapia
- Laboratory of Emerging Viruses, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
| | - Paulina Aguilera‐Cortés
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- HIV/AIDS Work Group, Faculty of MedicineUniversidad de ChileSantiagoChile
| | - Santiago Valenzuela
- Laboratory of Environmental Virology, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
| | - Fernando Valiente‐Echeverría
- SARS‐CoV‐2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- HIV/AIDS Work Group, Faculty of MedicineUniversidad de ChileSantiagoChile
| | - Ricardo Soto‐Rifo
- SARS‐CoV‐2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- HIV/AIDS Work Group, Faculty of MedicineUniversidad de ChileSantiagoChile
| | - Aldo Gaggero
- SARS‐CoV‐2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- Laboratory of Environmental Virology, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
| | - Gonzalo P. Barriga
- SARS‐CoV‐2 Research Group, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
- Laboratory of Emerging Viruses, Virology Program, Institute of Biomedical Sciences, Faculty of MedicineUniversidad de ChileSantiagoChile
| |
Collapse
|
7
|
Das M, Das A, Giri B, Sarkar R, Saha S. Habitat vulnerability in slum areas of India - What we learnt from COVID-19? INTERNATIONAL JOURNAL OF DISASTER RISK REDUCTION : IJDRR 2021; 65:102553. [PMID: 34513585 PMCID: PMC8421084 DOI: 10.1016/j.ijdrr.2021.102553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/15/2021] [Accepted: 09/01/2021] [Indexed: 05/09/2023]
Abstract
UN-Habitat identified the present COVID-19 pandemic as 'city-centric'. In India, more than 50% of the total cases were documented in megacities and million-plus cities. The slums of cities are the most vulnerable due to its unhygienic environment and high population density that requires an urgent implementation of public healthcare measures. This study aims to examine habitat vulnerability in slum areas to COVID-19 in India using principal component analysis and Fuzzy AHP based technique to develop slum vulnerability index to COVID-19 (SVIcovid-19). Four slum vulnerability groups (i.e. principal components) were retained with eigen-values greater than 1 based on Kaiser criterion - poor slum household status; lack of social distance maintenance; high concentrations of slum population and towns and mobility of the households. This study also mapped composite SVIcovid-19 on the basis of PCA and Fuzzy AHP method at the state level for a better understanding of spatial variations. The result shows that slums located in the eastern and central parts of India (particularly Uttar Pradesh, Bihar, Jharkhand, Odisha, West Bengal) were more vulnerable to COVID-19 transmission due to lack of availability as well as accessibility to the basic services and amenities to slum dwellers. Thus, the findings of the study may not only help to understand the habitat vulnerability in slum areas to COVID-19 but it will also teach a lesson to implement effective policies for enhancing the quality of slum households (HHs) and to reduce the health risk from any infectious disease in future.
Collapse
Affiliation(s)
- Manob Das
- Department of Geography, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Arijit Das
- Department of Geography, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Biplab Giri
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Raju Sarkar
- Department of Civil Engineering, Delhi Technological University, Delhi, 110042, India
| | - Sunil Saha
- Department of Geography, University of Gour Banga, Malda, 732103, West Bengal, India
| |
Collapse
|
8
|
Agca H, Akalin H, Saglik I, Hacimustafaoglu M, Celebi S, Ener B. Changing epidemiology of influenza and other respiratory viruses in the first year of COVID-19 pandemic. J Infect Public Health 2021; 14:1186-1190. [PMID: 34399190 DOI: 10.1016/j.jiph.2021.08.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/15/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022] Open
Abstract
INTRODUCTION We aimed to determine the epidemiological change in influenza and other respiratory tract viruses isolated from patients with nasopharyngeal swab samples in our hospital during the COVID-19 period. METHODS We investigated nasopharyngeal swabs for respiratory viruses between March 2020 and February 2021 during the first year of pandemic in Turkey. We used QIAStat Dx Respiratory panel (Qiagen, Germany) in QIAStat Dx (Qiagen, Germany) for detection of respiratory viruses between March 2020 and February 2021. Respiratory panel kit included influenza A, B, influenza A H1N1, rhinovirus/enterovirus, parainfluenza (PIV) 1,2,3,4, coronaviruses (CoVs) NL 63, 229E, OC43 and HKU1, human metapneumovirus (MPV) A/B, bocavirus, respiratory syncytial virus (RSV) A/B and adenovirus. RESULTS We retrospectively analyzed the results of 319 nasopharyngeal swab samples. The average age of 199 (62.4%) male and 120 (37.6%) female patients between the ages of 0-92 was 16 years. We found that 101 (31.7%) samples were positive for viruses. Rhino/enteroviruses were the most common viruses in all age groups. Influenza positivity rate during the first year of pandemic declined to 2.3% from 17.3% among the previous year. MPV infection activity did not change during the pandemic. DISCUSSION According to our findings we argue that epidemiology of respiratory viruses has changed during the pandemic period. Despite the current clinical focus on the COVID-19 pandemic, clinicians should keep in mind that rhino/enterovirus and MPV infections may mimic COVID-19 and respiratory infections should be differentially diagnosed with rapid multiplex kits containing SARS-CoV-2, rhino/enterovirus and MPV.
Collapse
Affiliation(s)
- Harun Agca
- Department of Medical Microbiology, Faculty of Medicine, Bursa Uludag University, Turkey.
| | - Halis Akalin
- Department of Infectıous Diseases and Clinical Microbiology, Faculty of Medicine, Bursa Uludag University, Turkey
| | - Imran Saglik
- Department of Medical Microbiology, Faculty of Medicine, Bursa Uludag University, Turkey
| | - Mustafa Hacimustafaoglu
- Department of Pediatrics, Infectious Diseases Subunit, Faculty of Medicine, Bursa Uludag University, Turkey
| | - Solmaz Celebi
- Department of Pediatrics, Infectious Diseases Subunit, Faculty of Medicine, Bursa Uludag University, Turkey
| | - Beyza Ener
- Department of Medical Microbiology, Faculty of Medicine, Bursa Uludag University, Turkey
| |
Collapse
|
9
|
Haage V, Ferreira de Oliveira-Filho E, Moreira-Soto A, Kühne A, Fischer C, Sacks JA, Corman VM, Müller MA, Drosten C, Drexler JF. Impaired performance of SARS-CoV-2 antigen-detecting rapid diagnostic tests at elevated and low temperatures. J Clin Virol 2021; 138:104796. [PMID: 33773413 PMCID: PMC7962993 DOI: 10.1016/j.jcv.2021.104796] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/14/2021] [Indexed: 12/24/2022]
Abstract
Analytical sensitivity of SARS-CoV-2 Ag-RDTs ranges from 1.0 × 106-5.5 × 107 copies/mL. Even short-term exposure to 37 °C reduces sensitivity of SARS-CoV-2 Ag-RDTs. Elevated temperatures impair sensitivity at clinically relevant virus concentrations. Low temperatures limit SARS-CoV-2 Ag-RDT specificity. Storage and operation of SARS-CoV-2 Ag-RDTs at recommended conditions is essential.
Antigen-detecting rapid diagnostic tests (Ag-RDTs) can complement molecular diagnostics for COVID-19. The recommended temperature for storage of SARS-CoV-2 Ag-RDTs ranges between 2−30 °C. In the global South, mean temperatures can exceed 30 °C. In the global North, Ag-RDTs are often used in external testing facilities at low ambient temperatures. We assessed analytical sensitivity and specificity of eleven commercially-available SARS-CoV-2 Ag-RDTs using different storage and operational temperatures, including short- or long-term storage and operation at recommended temperatures or at either 2−4 °C or at 37 °C. The limits of detection of SARS-CoV-2 Ag-RDTs under recommended conditions ranged from 1.0×106- 5.5×107 genome copies/mL of infectious SARS-CoV-2 cell culture supernatant. Despite long-term storage at recommended conditions, 10 min pre-incubation of Ag-RDTs and testing at 37 °C resulted in about ten-fold reduced sensitivity for five out of 11 SARS-CoV-2 Ag-RDTs, including both Ag-RDTs currently listed for emergency use by the World Health Organization. After 3 weeks of storage at 37 °C, eight of the 11 SARS-CoV-2 Ag-RDTs exhibited about ten-fold reduced sensitivity. Specificity of SARS-CoV-2 Ag-RDTs using cell culture supernatant from common respiratory viruses was not affected by storage and testing at 37 °C, whereas false-positive results occurred at outside temperatures of 2−4 °C for two out of six tested Ag-RDTs, again including an Ag-RDT recommended by the WHO. In summary, elevated temperatures impair sensitivity, whereas low temperatures impair specificity of SARS-CoV-2 Ag-RDTs. Consequences may include false-negative test results at clinically relevant virus concentrations compatible with transmission and false-positive results entailing unwarranted quarantine assignments. Storage and operation of SARS-CoV-2 Ag-RDTs at recommended conditions is essential for successful usage during the pandemic.
Collapse
Affiliation(s)
- Verena Haage
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Edmilson Ferreira de Oliveira-Filho
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andres Moreira-Soto
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Arne Kühne
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carlo Fischer
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jilian A Sacks
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Charité-Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
10
|
Tozetto-Mendoza TR, Kanunfre KA, Vilas-Boas LS, Sanchez Espinoza EP, Paião HGO, Rocha MC, de Paula AV, de Oliveira MS, Zampelli DB, Vieira JM, Buss L, Costa SF, Sabino EC, Witkin SS, Okay TS, Mendes-Correa MC. Nucleoprotein-based ELISA for detection of SARS-COV-2 IgG antibodies: Could an old assay be suitable for serodiagnosis of the new coronavirus? J Virol Methods 2021; 290:114064. [PMID: 33453299 PMCID: PMC7804377 DOI: 10.1016/j.jviromet.2021.114064] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/22/2020] [Accepted: 01/10/2021] [Indexed: 01/14/2023]
Abstract
Objectives We evaluated the performance of a nucleoprotein-based enzyme-linked immunosorbent assay (ELISA) for detection of IgG antibodies to SARS-CoV-2. Methods The ELISA was based on serum IgG reactivity to a 46-kDa protein derived from the recombinant SARS-CoV2 nucleoprotein. Assay sensitivity was assessed using serum samples from 134 COVID-19 confirmed cases obtained > 15 days after symptom onset. Specificity was determined by testing sera from 94 healthy controls. Cross-reactivity was evaluated with sera from 96 individuals with previous dengue or zika virus-confirmed infections, with 44 sera from individuals with confirmed infections to other respiratory viruses or with bacterial and fungal infections that cause pneumonia and with 40 sera negative for SARS-CoV-2 nucleoprotein by commercial ELISA kits. Results The majority of subjects were male and ≥ 60 years old. Assay sensitivity was 90.3 % (95 % confidence interval 84.1 %–94.2 %) and specificity was 97.9 % (92.6 %–99.4 %). There was no cross-reactivity with sera from individuals diagnosed with dengue, zika virus, influenza virus, rhinovirus, adenovirus, respiratory syncytial virus, seasonal coronavirus, Mycobacterium tuberculosis, Staphylococcus (S. aureus and coagulase-negative), Streptococcus pneumoniae, Klebsiella pneumoniae and the fungus Aspergillus fumigatus. The level of concordance of our test with results from commercial ELISA kits was 100 %. Conclusion The nucleoprotein-based ELISA was specific for detection of IgG anti-nucleoprotein antibodies to SARS-CoV-2. It utilizes a frequently employed low expense assay protocol and is easier to perform than other currently available commercial SARS-CoV2 antibody detection tests.
Collapse
Affiliation(s)
| | - Kelly Aparecida Kanunfre
- LIM-48, Clinical Hospital, School of Medicine, University of São Paulo, Brazil; Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine, School of Medicine, University of São Paulo, Brazil
| | - Lucy Santos Vilas-Boas
- LIM-52, Institute of Tropical Medicine, School of Medicine, Clinical Hospital, University of São Paulo, Brazil
| | - Evelyn Patricia Sanchez Espinoza
- LIM-49, Institute of Tropical Medicine, School of Medicine, University of São Paulo, Brazil; Department of Infection Diseases, Clinical Hospital, School of Medicine, University of São Paulo, Brazil
| | - Heuder Gustavo Oliveira Paião
- LIM-52, Institute of Tropical Medicine, School of Medicine, Clinical Hospital, University of São Paulo, Brazil; Department of Infection Diseases, Clinical Hospital, School of Medicine, University of São Paulo, Brazil
| | - Mussya Cisotto Rocha
- LIM-48, Clinical Hospital, School of Medicine, University of São Paulo, Brazil; Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine, School of Medicine, University of São Paulo, Brazil
| | - Anderson Vicente de Paula
- LIM-52, Institute of Tropical Medicine, School of Medicine, Clinical Hospital, University of São Paulo, Brazil
| | - Maura Salaroli de Oliveira
- Department of Infection control- Clinical Hospital, School of Medicine, University of São Paulo, Brazil; Hospital Sírio Libanês, Brazil
| | | | | | - Lewis Buss
- Department of Infection Diseases, Clinical Hospital, School of Medicine, University of São Paulo, Brazil
| | - Silvia Figueiredo Costa
- LIM-49, Institute of Tropical Medicine, School of Medicine, University of São Paulo, Brazil; Department of Infection Diseases, Clinical Hospital, School of Medicine, University of São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Department of Infection Diseases, Clinical Hospital, School of Medicine, University of São Paulo, Brazil; LIM-46, Institute of Tropical Medicine, School of Medicine, University of São Paulo, Brazil
| | - Steven S Witkin
- LIM-52, Institute of Tropical Medicine, School of Medicine, Clinical Hospital, University of São Paulo, Brazil; Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, New York, United States
| | - Thelma Suely Okay
- Laboratory of Seroepidemiology and Immunobiology, Institute of Tropical Medicine, School of Medicine, University of São Paulo, Brazil; Department of Pediatrics, School of Medicine, University of São Paulo, Brazil
| | - Maria Cassia Mendes-Correa
- LIM-52, Institute of Tropical Medicine, School of Medicine, Clinical Hospital, University of São Paulo, Brazil; Department of Infection Diseases, Clinical Hospital, School of Medicine, University of São Paulo, Brazil
| |
Collapse
|
11
|
Abstract
Community protective immunity can affect RNA virus evolution by selecting for new antigenic variants on the scale of years, exemplified by the need of annual evaluation of influenza vaccines. The extent to which this process termed antigenic drift affects coronaviruses remains unknown. Alike the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), seasonal human coronaviruses (HCoV) likely emerged from animal reservoirs as new human pathogens in the past. We therefore analyzed the long-term evolutionary dynamics of the ubiquitous HCoV-229E and HCoV-OC43 in comparison with human influenza A virus (IAV) subtype H3N2. We focus on viral glycoprotein genes that mediate viral entry into cells and are major targets of host neutralizing antibody responses. Maximum likelihood and Bayesian phylogenies of publicly available gene datasets representing about three decades of HCoV and IAV evolution showed that all viruses had similar ladder-like tree shapes compatible with antigenic drift, supported by different tree shape statistics. Evolutionary rates inferred in a Bayesian framework were 6.5 × 10-4 (95% highest posterior density (HPD), 5.4-7.5 × 10-4) substitutions per site per year (s/s/y) for HCoV-229E spike (S) genes and 5.7 × 10-4 (95% HPD, 5-6.5 × 10-4) s/s/y for HCoV-OC43 S genes, which were about fourfold lower than the 2.5 × 10-3 (95% HPD, 2.3-2.7 × 10-3) s/s/y rate for IAV hemagglutinin (HA) genes. Coronavirus S genes accumulated about threefold less (P < 0.001) non-synonymous mutations (dN) over time than IAV HA genes. In both IAV and HCoV, the average rate of dN within the receptor binding domains (RBD) was about fivefold higher (P < 0.0001) than in other glycoprotein gene regions. Similarly, most sites showing evidence for positive selection occurred within the RBD (HCoV-229E, 6/14 sites, P < 0.05; HCoV-OC43, 23/38 sites, P < 0.01; IAV, 13/15 sites, P = 0.08). In sum, the evolutionary dynamics of HCoV and IAV showed several similarities, yet amino acid changes potentially representing antigenic drift occurred on a lower scale in endemic HCoV compared to IAV. It seems likely that pandemic SARS-CoV-2 evolution will bear similarities with IAV evolution including accumulation of adaptive changes in the RBD, requiring vaccines to be updated regularly, whereas higher SARS-CoV-2 evolutionary stability resembling endemic HCoV can be expected in the post-pandemic stage.
Collapse
Affiliation(s)
- Wendy K Jo
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
| | - Christian Drosten
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), associated partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Felix Drexler
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), associated partner Charité-Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
12
|
Fernández-Raga M, Díaz-Marugán L, García Escolano M, Bort C, Fanjul V. SARS-CoV-2 viability under different meteorological conditions, surfaces, fluids and transmission between animals. ENVIRONMENTAL RESEARCH 2021; 192:110293. [PMID: 33017611 PMCID: PMC7531924 DOI: 10.1016/j.envres.2020.110293] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 05/17/2023]
Abstract
Since the COVID-19 outbreak, researchers have tried to characterise the novel coronavirus SARS-CoV-2 to better understand the pathogenic mechanisms of the virus and prevent further dissemination. As a consequence, there has been a bloom in scientific research papers focused on the behaviour of the virus in different environmental contexts. Nevertheless, despite these efforts and due to its novelty, available information about this coronavirus is limited, as several research studies are still ongoing. This review aims to shed light on this issue. To that end, we have examined the scientific literature to date regarding the viability of SARS-CoV-2 on surfaces and fluids or under different environmental conditions (temperature, precipitation and UV radiation). We have also addressed the role of animals in the transmission of this coronavirus.
Collapse
Affiliation(s)
- María Fernández-Raga
- IMARENAB, Applied Chemical and Physics Department, University of León, Spain; Celera Talent Association, Madrid, Spain.
| | | | - Marta García Escolano
- Celera Talent Association, Madrid, Spain; Prospera Biotech. Scientific Park Universitas Miguel Hernández, Elche, Spain
| | - Carlos Bort
- Celera Talent Association, Madrid, Spain; Xplore.ai, Madrid, Spain
| | - Víctor Fanjul
- Celera Talent Association, Madrid, Spain; Data Team, Savana Medica, Madrid, Spain
| |
Collapse
|
13
|
Araujo DB, Machado RRG, Amgarten DE, Malta FDM, de Araujo GG, Monteiro CO, Candido ED, Soares CP, de Menezes FG, Pires ACC, Santana RAF, Viana ADO, Dorlass E, Thomazelli L, Ferreira LCDS, Botosso VF, Carvalho CRG, Oliveira DBL, Pinho JRR, Durigon EL. SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network. Mem Inst Oswaldo Cruz 2020; 115:e200342. [PMID: 33111751 PMCID: PMC7586445 DOI: 10.1590/0074-02760200342] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. OBJECTIVES The objective of this work is to describe the isolation and propagation properties of SARS-CoV-2 isolates from the first confirmed cases of coronavirus disease 2019 (COVID-19) in Brazil. METHODS After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks - viable (titre 2.11 × 106 TCID50/mL, titre 1.5 × 106 PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. MAIN CONCLUSION We believe that the protocols for virus growth and studies here described and the distribution initiative may constitute a viable model for other developing countries, not only to help a rapid effective pandemic response, but also to facilitate and support basic scientific research.
Collapse
Affiliation(s)
- Danielle Bastos Araujo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil.,Hospital Israelita Albert Einstein, São Paulo, SP, Brasil
| | | | | | | | - Gabriel Guarany de Araujo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Cairo Oliveira Monteiro
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Erika Donizetti Candido
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Camila Pereira Soares
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | | | | | | | - Amanda de Oliveira Viana
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Erick Dorlass
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | - Luciano Thomazelli
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil
| | | | - Viviane Fongaro Botosso
- Instituto Butantã, Centro de Inovação e Desenvolvimento, Laboratório de Virologia, São Paulo, SP, Brasil
| | | | - Danielle Bruna Leal Oliveira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil.,Hospital Israelita Albert Einstein, São Paulo, SP, Brasil.,Instituto Butantã, Centro de Inovação e Desenvolvimento, Laboratório de Virologia, São Paulo, SP, Brasil
| | - João Renato Rebello Pinho
- Hospital Israelita Albert Einstein, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Patologia, Laboratório de Medicina Laboratorial (LIM/03), São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, Laboratório de Gastroenterologia Clínica e Experimental (LIM/07), São Paulo, SP, Brasil
| | - Edison Luiz Durigon
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brasil.,Plataforma Científica Pasteur-USP, São Paulo, SP, Brasil
| |
Collapse
|
14
|
Rucinski SL, Binnicker MJ, Thomas AS, Patel R. Seasonality of Coronavirus 229E, HKU1, NL63, and OC43 From 2014 to 2020. Mayo Clin Proc 2020; 95:1701-1703. [PMID: 32753142 PMCID: PMC7275147 DOI: 10.1016/j.mayocp.2020.05.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 12/05/2022]
Abstract
The possibility of seasonality of COVID-19 is being discussed; we show clinical microbiology laboratory data illustrating seasonality of coronaviruses 229E, HKU1, NL63, and OC43. The data shown are specific to the 4 studied coronaviruses and may or may not generalize to COVID-19.
Collapse
Affiliation(s)
- Stefanea L Rucinski
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew J Binnicker
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Amber S Thomas
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
15
|
Raoult D, Zumla A, Locatelli F, Ippolito G, Kroemer G. Coronavirus infections: Epidemiological, clinical and immunological features and hypotheses. Cell Stress 2020; 4:66-75. [PMID: 32292881 PMCID: PMC7064018 DOI: 10.15698/cst2020.04.216] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronaviruses (CoVs) are a large family of enveloped, positive-strand RNA viruses. Four human CoVs (HCoVs), the non-severe acute respiratory syndrome (SARS)-like HCoVs (namely HCoV 229E, NL63, OC43, and HKU1), are globally endemic and account for a substantial fraction of upper respiratory tract infections. Non-SARS-like CoV can occasionally produce severe diseases in frail subjects but do not cause any major (fatal) epidemics. In contrast, SARS like CoVs (namely SARS-CoV and Middle-East respiratory syndrome coronavirus, MERS-CoV) can cause intense short-lived fatal outbreaks. The current epidemic caused by the highly contagious SARS-CoV-2 and its rapid spread globally is of major concern. There is scanty knowledge on the actual pandemic potential of this new SARS-like virus. It might be speculated that SARS-CoV-2 epidemic is grossly underdiagnosed and that the infection is silently spreading across the globe with two consequences: (i) clusters of severe infections among frail subjects could haphazardly occur linked to unrecognized index cases; (ii) the current epidemic could naturally fall into a low-level endemic phase when a significant number of subjects will have developed immunity. Understanding the role of paucisymptomatic subjects and stratifying patients according to the risk of developing severe clinical presentations is pivotal for implementing reasonable measures to contain the infection and to reduce its mortality. Whilst the future evolution of this epidemic remains unpredictable, classic public health strategies must follow rational patterns. The emergence of yet another global epidemic underscores the permanent challenges that infectious diseases pose and underscores the need for global cooperation and preparedness, even during inter-epidemic periods.
Collapse
Affiliation(s)
- Didier Raoult
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005 Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Alimuddin Zumla
- Division of Infection and Immunity, Center for Clinical Microbiology, University College London, London, UK.,The National Institute of Health Research Biomedical Research Centre at UCL Hospitals, London, UK
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases, Lazzaro Spallanzani, IRCCS, Rome, Italy
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
16
|
Góes LGB, Zerbinati RM, Tateno AF, de Souza AV, Ebach F, Corman VM, Moreira-Filho CA, Durigon EL, da Silva Filho LVRF, Drexler JF. Typical epidemiology of respiratory virus infections in a Brazilian slum. J Med Virol 2019; 92:1316-1321. [PMID: 31769524 PMCID: PMC7228228 DOI: 10.1002/jmv.25636] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/21/2019] [Indexed: 02/01/2023]
Abstract
Host population size, density, immune status, age structure, and contact rates are critical elements of virus epidemiology. Slum populations stand out from other settings and may present differences in the epidemiology of acute viral infections. We collected nasopharyngeal specimens from 282 children aged ≤5 years with acute respiratory tract infection (ARI) during 2005 to 2006 in one of the largest Brazilian slums. We conducted real‐time reverse transcription‐polymerase chain reaction (RT‐PCR) for 16 respiratory viruses, nested RT‐PCR‐based typing of rhinoviruses (HRVs), and collected clinical symptoms. Viruses were common causes of respiratory disease; with ≥1 virus being detected in 65.2% of patients. We detected 15 different viruses during 1 year with a predominance of HRV (33.0%) and human respiratory syncytial virus (hRSV, 12.1%) infections, and a high rate of viral coinfections (28.3%). We observed seasonality of hRSV, HRV and human coronavirus infections, more severe symptoms in hRSV and influenza virus (FLU) infections and prolonged circulation of seven HRV clusters likely representing distinct serotypes according to genomic sequence distances. Potentially unusual findings included the absence of human metapneumovirus detections and lack of typical FLU seasonal patterns, which may be linked to the population size and density of the slum. Nonetheless, most epidemiological patterns were similar to other studies globally, suggesting surprising similarities of virus‐associated ARI across highly diverse settings and a complex impact of population characteristics on respiratory virus epidemiology. Large epidemiological study of respiratory viruses in children from one of the biggest Brazilian slums using sensitive molecular PCR assays Viruses are common causes of respiratory disease in pediatric patients from a Brazilian slum 15 distinct viruses circulate in the Brazilian slum, with highest prevalence of rhinoviruses and human respiratory syncytial virus The epidemiology of virus‐associated respiratory infections presents surprising similarities worldwide despite drastic differences in socioeconomic status and population characteristics
Collapse
Affiliation(s)
- Luiz Gustavo Bentim Góes
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Laboratório de Virologia Clínica e Molecular, Departamento de Microbiologia - ICB-II, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Fabian Ebach
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany
| | | | - Edison Luiz Durigon
- Laboratório de Virologia Clínica e Molecular, Departamento de Microbiologia - ICB-II, Universidade de São Paulo, São Paulo, Brazil
| | | | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, Russia
| |
Collapse
|