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Luštrek M, Cesar Z, Suljič A, Kogoj R, Knap N, Virant MJ, Uršič T, Petrovec M, Avšič-Županc T, Korva M. Influenza A, Influenza B, human respiratory syncytial virus and SARSCoV-2 molecular diagnostics and epidemiology in the post COVID-19 era. Respir Res 2024; 25:234. [PMID: 38840154 PMCID: PMC11151539 DOI: 10.1186/s12931-024-02862-7] [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: 12/21/2023] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The concurrent circulation of SARS-CoV-2 with other respiratory viruses is unstoppable and represents a new diagnostic reality for clinicians and clinical microbiology laboratories. Multiplexed molecular testing on automated platforms that focus on the simultaneous detection of multiple respiratory viruses in a single tube is a useful approach for current and future diagnosis of respiratory infections in the clinical setting. METHODS Two time periods were included in the study: from February to April 2022, an early 2022 period, during the gradual lifting of COVID-19 prevention measures in the country, and from October 2022 to April 2023, the 2022/23 respiratory infections season. We analysed a total of 1,918 samples in the first period and 18,131 respiratory samples in the second period using a multiplex molecular assay for the simultaneous detection of Influenza A (Flu-A), Influenza B (Flu-B), Human Respiratory Syncytial Virus (HRSV) and SARS-CoV-2. RESULTS The results from early 2022 showed a strong dominance of SARS-CoV-2 infections with 1,267/1,918 (66.1%) cases. Flu-A was detected in 30/1,918 (1.6%) samples, HRSV in 14/1,918 (0.7%) samples, and Flu-B in 2/1,918 (0.1%) samples. Flu-A/SARS-CoV-2 co-detections were observed in 11/1,267 (0.9%) samples, and HRSV/SARS-CoV-2 co-detection in 5/1,267 (0.4%) samples. During the 2022/23 winter respiratory season, SARS-CoV-2 was detected in 1,738/18,131 (9.6%), Flu-A in 628/18,131 (3.5%), Flu-B in 106/18,131 (0.6%), and HRSV in 505/18,131 (2.8%) samples. Interestingly, co-detections were present to a similar extent as in early 2022. CONCLUSION The results show that the multiplex molecular approach is a valuable tool for the simultaneous laboratory diagnosis of SARS-CoV-2, Flu-A/B, and HRSV in hospitalized and outpatients. Infections with Flu-A/B, and HRSV occurred shortly after the COVID-19 control measures were lifted, so a strong reoccurrence of various respiratory infections and co-detections in the post COVID-19 period was to be expected.
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Affiliation(s)
- Manca Luštrek
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Zala Cesar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Alen Suljič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Monika Jevšnik Virant
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Tina Uršič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia.
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Cho HJ, Rhee JE, Kang D, Choi EH, Lee NJ, Woo S, Lee J, Lee SW, Kim EJ, Yun KW. Epidemiology of Respiratory Viruses in Korean Children Before and After the COVID-19 Pandemic: A Prospective Study From National Surveillance System. J Korean Med Sci 2024; 39:e171. [PMID: 38769924 PMCID: PMC11106558 DOI: 10.3346/jkms.2024.39.e171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/23/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic led to a decrease in the seasonal incidence of many respiratory viruses worldwide due to the impact of nonpharmaceutical interventions (NPIs). However, as NPI measures were relaxed, respiratory viral infections re-emerged. We aimed to characterize the epidemiology of respiratory viruses in Korean children during post-COVID-19 pandemic years compared to that before the pandemic. METHODS A nationwide prospective ongoing surveillance study has been conducted for detection of respiratory viruses between January 2017 and June 2023. We included data on adenovirus (AdV), human bocavirus (HBoV), human coronavirus (HCoV), human metapneumovirus (HMPV), human rhinovirus (HRV), influenza virus (IFV), parainfluenza virus (PIV), and respiratory syncytial virus (RSV), which were detected in children and adolescents younger than 20 years. We analyzed the weekly detection frequency of individual viruses and the age distribution of the affected children. The study period was divided into prepandemic (2017-2019) and postpandemic (2021-2023) periods. RESULTS A total of 19,589 and 14,068 samples were collected in the pre- and postpandemic periods, respectively. The overall detection rate of any virus throughout the study period was 63.1%, with the lowest occurring in the 2nd half of 2020 (50.6%) and the highest occurring in the 2nd half of 2021 (72.3%). Enveloped viruses (HCoV, HMPV, IFV, PIV, and RSV) almost disappeared, but nonenveloped viruses (AdV, HBoV, and HRV) were detected even during the peak of the COVID-19 pandemic. The codetection rate increased from 15.0% prepandemic to 19.1% postpandemic (P < 0.001). During the postpandemic period, a large out-of-season PIV and HMPV epidemic occurred, but the usual seasonality began to be restored in 2023. The mean age of children with each virus detected in 2023 was significantly greater than that in prepandemic years (P = 0.003 and 0.007 for AdV and HCoV, respectively; P < 0.001 for others). The mean age of children with IFV increased in 2022 (11.1 ± 5.2 years) from prepandemic years (7.9 ± 4.6 years) but decreased to 8.7 ± 4.1 years in 2023. CONCLUSION With the relaxation of NPI measures, several seasonal respiratory viruses cocirculated with unusual seasonal epidemic patterns and were associated with increasing age of infected children.
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Affiliation(s)
- Hyo Jin Cho
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
- Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jee Eun Rhee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - Dayun Kang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Nam-Joo Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - SangHee Woo
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - Jaehee Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - Sang-Won Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea.
| | - Ki Wook Yun
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea.
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Berry GJ, Jhaveri TA, Larkin PMK, Mostafa H, Babady NE. ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses. J Appl Lab Med 2024; 9:599-628. [PMID: 38695489 DOI: 10.1093/jalm/jfae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 06/06/2024]
Abstract
Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.
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Affiliation(s)
- Gregory J Berry
- Columbia University Vagelos College of Physicians and Surgeons, New York-Presbyterian-Columbia University Irving Medical Center, New York, NY, United States
| | - Tulip A Jhaveri
- Department of Internal Medicine, Division of Infectious Diseases, University of Mississippi Medical Center, Jackson, MS, United States
| | - Paige M K Larkin
- University of Chicago Pritzker School of Medicine, NorthShore University Health System, Chicago, IL, United States
| | - Heba Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Baltimore, MD, United States
| | - N Esther Babady
- Clinical Microbiology and Infectious Disease Services, Department of Pathology and Laboratory Medicine and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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Vink E, Banda L, Amoah AS, Kasenda S, Read JM, Jewell C, Denis B, Mwale AC, Crampin A, Anscombe C, Menyere M, Ho A. Prevalence of Endemic Respiratory Viruses During the COVID-19 Pandemic in Urban and Rural Malawi. Open Forum Infect Dis 2024; 11:ofad643. [PMID: 38312213 PMCID: PMC10836885 DOI: 10.1093/ofid/ofad643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 02/06/2024] Open
Abstract
Background We investigated endemic respiratory virus circulation patterns in Malawi, where no lockdown was imposed, during the COVID-19 pandemic. Methods Within a prospective household cohort in urban and rural Malawi, adult participants provided upper respiratory tract (URT) samples at 4 time points between February 2021 and April 2022. Polymerase chain reaction (PCR) was performed for SARS-CoV-2, influenza, and other endemic respiratory viruses. Results 1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) samples were PCR- positive for >1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most common. No influenza A virus was detected. Influenza B and respiratory syncytial virus (RSV) were rare. Higher virus positivity were detected in the rural setting and at earlier time points. Coinfections were infrequent. Conclusions Endemic respiratory viruses circulated in the community in Malawi during the pandemic, though influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts.
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Affiliation(s)
- Elen Vink
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Louis Banda
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
| | - Abena S Amoah
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
- Department of Population Health, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Leiden University Medical Center, Leiden, the Netherlands
| | - Stephen Kasenda
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
| | - Jonathan M Read
- Centre for Health Information Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Chris Jewell
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | - Amelia Crampin
- Malawi Epidemiology and Intervention Research Unit, Lilongwe and Chilumba, Malawi
- Department of Population Health, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Catherine Anscombe
- Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
- Liverpool School of Tropical Medicine, University of Liverpool, Liverpool, UK
| | - Mavis Menyere
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Chan CM, Wahab AA, Ali A. Assessing the impact of COVID-19 on epidemiological changes of severe pediatric respiratory syncytial virus infections in Malaysia. Front Public Health 2024; 12:1246921. [PMID: 38356949 PMCID: PMC10866006 DOI: 10.3389/fpubh.2024.1246921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Respiratory syncytial virus (RSV) is one of the leading causes of hospitalization and mortality among children with respiratory tract infections. The non-pharmaceutical preventive measures against severe acute respiratory syndrome coronavirus (COVID-19) may have reduced the transmission of RSV, altering its tropical epidemiological seasonality. Thus, this study represents the first attempt to evaluate changes in RSV epidemiology in the context of COVID-19 pandemic in Malaysia. Methods Conducted at a tertiary hospital in Kuala Lumpur, Malaysia, this retrospective study analyzed collated data of children aged <12 years who were admitted for severe respiratory infections from 2017 to 2022. Time series models were used to predict the differences between actual and forecasted RSV cases, while logistic regression assessed the statistical association between RSV and COVID-19. Results Among the 4,084 children analyzed, we reported a significant inverse relationship between RSV and COVID-19 infections during the pandemic (2020-2021) (p < 0.05). In 2020, the RSV positivity rate sharply declined to 8.3 and 5.9%, respectively, in the two prominent seasons. Time series analysis showed a tremendous decrease in cases compared to the expected values, with reductions of 98.3% in the first season and 95.7% in the second season. However, following the lifting of the restriction order in 2022, RSV infections rose sharply with a positivity rate of 36.3%, higher than pre-COVID-19 pandemic levels. Conclusion This study provides evidence of increasing RSV cases post-COVID-19 pandemic, due to immunity debt. Hence, the healthcare system must be prepared to address future RSV outbreaks with the appropriate implementation of prophylaxis and public health measures.
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Affiliation(s)
- Chee Mun Chan
- Department of Pediatrics, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Research Center, Hospital Tunku Ampuan Besar Tuanku Aishah Rohani, UKM Specialist Children’s Hospital, Kuala Lumpur, Malaysia
| | - Asrul Abdul Wahab
- Department of Microbiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Adli Ali
- Department of Pediatrics, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Research Center, Hospital Tunku Ampuan Besar Tuanku Aishah Rohani, UKM Specialist Children’s Hospital, Kuala Lumpur, Malaysia
- Institute of IR4.0, Universiti Kebangsaan Malaysia, Bangi, Malaysia
- Infection and Immunology Health and Advanced Medicine Cluster, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Fall A, Han L, Yunker M, Gong YN, Li TJ, Norton JM, Abdullah O, Rothman RE, Fenstermacher KZJ, Morris CP, Pekosz A, Klein E, Mostafa HH. Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021-2023. Open Forum Infect Dis 2023; 10:ofad577. [PMID: 38088981 PMCID: PMC10715682 DOI: 10.1093/ofid/ofad577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Background The circulation and the genomic evolution of influenza A(H3N2) viruses during the 2021/2022 and 2022/2023 seasons were studied and associated with infection outcomes. Methods Remnant influenza A-positive samples following standard-of-care testing from patients across the Johns Hopkins Health System (JHHS) were used for the study. Samples were randomly selected for whole viral genome sequencing. The sequence-based pEpitope model was used to estimate the predicted vaccine efficacy (pVE) for circulating H3N2 viruses. Clinical data were collected and associated with viral genomic data. Results A total of 121 683 respiratory specimens were tested for influenza at JHHS between 1 September 2021 and 31 December 2022. Among them, 6071 (4.99%) tested positive for influenza A. Of these, 805 samples were randomly selected for sequencing, with hemagglutinin (HA) segments characterized for 610 samples. Among the characterized samples, 581 were H3N2 (95.2%). Phylogenetic analysis of HA segments revealed the exclusive circulation of H3N2 viruses with HA segments of the 3C.2a1b.2a.2 clade. Analysis of a total of 445 complete H3N2 genomes revealed reassortments; 200 of 227 of the 2022/2023 season genomes (88.1%) were found to have reassorted with clade 3C.2a1b.1a. The pVE was estimated to be -42.53% for the 2021/2022 season and 30.27% for the 2022/2023 season. No differences in clinical presentations or admissions were observed between the 2 seasons. Conclusions The increased numbers of cases and genomic diversity of influenza A(H3N2) during the 2022/2023 season were not associated with a change in disease severity compared to the previous influenza season.
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Affiliation(s)
- Amary Fall
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Lijie Han
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Madeline Yunker
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Tai-Jung Li
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Julie M Norton
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Omar Abdullah
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Richard E Rothman
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | | | - C Paul Morris
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Andrew Pekosz
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W.Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Eili Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, District of Columbia, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Ranno S, Coltella L, Linardos G, Di Maio VC, Colagrossi L, Gentile L, Galeno E, Ciofi Degli Atti ML, Cristaldi S, Villani A, Raponi M, Perno CF, Russo C. Influenza viruses circulation in a tertiary care children hospital in Rome: a comparison between 2022 and the previous 5 years. Ital J Pediatr 2023; 49:121. [PMID: 37705032 PMCID: PMC10500714 DOI: 10.1186/s13052-023-01519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/27/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Influenza surveillance aims to determine onset, duration and intensity of the seasonal Influence-like Illness (ILI); data collection begins in the week 42 of a year and ends in the week 17 of the following year. In this observational study, we report the experience of a tertiary care children hospital in Rome about Influenza viruses circulation during the calendar year 2022 (January-December) in comparison with the previous five years (2017-2021), with a special focus on the weeks 18-41, usually not under surveillance. METHODS This retrospective study involved 36782 respiratory samples referred to 21354 patients (pts), median age 2.63 years, admitted with respiratory symptoms at Bambino Gesù Children's Hospital in the years 2017-2022. Respiratory viruses were detected by molecular Allplex™ Respiratory Panel Assays (Seegene, Korea). RESULTS Regarding the pre pandemic years, 2017-2019, distribution of Flu positive patients focused in the first weeks of the year (weeks 1-17). During the pandemic period, Flu was not detected. In 2022, 239 Flu viruses were identified: 37 FluA (weeks 1-17), 29 FluA (weeks 18-41) and 168 FluA and 5 FluB (weeks 42-52). For the year 2022, during the non-epidemic period, the number of Flu viruses detected corresponded to 12.1% of total Flu detected, respect to 0-1.7% for the previous five years (p < 0.001). CONCLUSIONS When compared with pre SARS-CoV-2 pandemic years, our data show a significant increase in Influenza cases during weeks 18-41/2022 and reveal an unexpected summer circulation of these viruses: just weeks 26-30 showed to be influenza virus free. A national year-round Flu surveillance could be useful to understand if changing in influenza epidemiology is transitional or likely to persist in the following years.
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Affiliation(s)
- Stefania Ranno
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy
| | - Luana Coltella
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy.
| | - Giulia Linardos
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy
| | - Velia Chiara Di Maio
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy
| | - Luna Colagrossi
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy
| | - Leonarda Gentile
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy
| | - Eugenia Galeno
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy
| | - Marta Luisa Ciofi Degli Atti
- Epidemiology, Clinical Pathways and Clinical Risk, Medical Direction, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sebastian Cristaldi
- Pediatric Unit, Pediatric Emergency Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alberto Villani
- Pediatric Unit, Pediatric Emergency Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Carlo Federico Perno
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy
| | - Cristina Russo
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome, 00165, Italy
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King KL, Ham R, Smothers A, Lee I, Bowie T, Teetsel E, Peng C, Dean D. Repurposing a SARS-CoV-2 surveillance program for infectious respiratory diseases in a university setting. Front Public Health 2023; 11:1168551. [PMID: 37727605 PMCID: PMC10505707 DOI: 10.3389/fpubh.2023.1168551] [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: 02/17/2023] [Accepted: 08/16/2023] [Indexed: 09/21/2023] Open
Abstract
Standard multiplex RT-qPCR diagnostic tests use nasopharyngeal swabs to simultaneously detect a variety of infections, but commercially available kits can be expensive and have limited throughput. Previously, we clinically validated a saliva-based RT-qPCR diagnostic test for SARS-CoV-2 to provide low-cost testing with high throughput and low turnaround time on a university campus. Here, we developed a respiratory diagnostic panel to detect SARS-CoV-2, influenza A and B within a single saliva sample. When compared to clinical results, our assay demonstrated 93.5% accuracy for influenza A samples (43/46 concordant results) with no effect on SARS-CoV-2 accuracy or limit of detection. In addition, our assay can detect simulated coinfections at varying virus concentrations generated from synthetic RNA controls. We also confirmed the stability of influenza A in saliva at room temperature for up to 5 days. The cost of the assay is lower than standard nasopharyngeal swab respiratory panel tests as saliva collection does not require specialized swabs or trained clinical personnel. By repurposing the lab infrastructure developed for the COVID-19 pandemic, our multiplex assay can be used to provide expanded access to respiratory disease diagnostics, especially for community, school, or university testing applications where saliva testing was effectively utilized during the COVID-19 pandemic.
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Affiliation(s)
- Kylie L. King
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Rachel Ham
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Austin Smothers
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Isaac Lee
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Tyler Bowie
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Erika Teetsel
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Congyue Peng
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
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Cáceres C, Castillo M, Carrillo K, Tapia CV, Valderrama G, Maquilón C, Toro-Ascuy D, Zorondo-Rodríguez F, Fuenzalida LF. Overnutrition as a risk factor for more serious respiratory viral infections in children: A retrospective study in hospitalized patients. ENDOCRINOL DIAB NUTR 2023; 70:476-483. [PMID: 37527958 DOI: 10.1016/j.endien.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/03/2023] [Indexed: 08/03/2023]
Abstract
BACKGROUND The prevalence of obesity has increased dramatically in children worldwide. Obesity has been recognized as a risk factor for more serious viral respiratory infections, mainly in adults. OBJECTIVE To study the relationship between overnutrition (obesity and overweight) and clinical severity in children hospitalized with acute respiratory infections of viral origin. METHODS One hundred and forty-three clinical records of children between 2 and 18 years old hospitalized for acute respiratory infection at Clínica Dávila (2014-2018) were analyzed, recording the respiratory viruses detected at the time of hospitalization, weight, and height. Nutritional status was estimated using Z score or body mass index, according to age. RESULTS Eighty-tree3 children (58%) were positive for more than one respiratory virus. The main virus detected in monoinfection was adenovirus (9.8%), followed by respiratory syncytial virus (7.7%) and parainfluenza virus (7.7%). There were no deaths. Patients with obesity presented more days of hospitalization (P = .04), oxygen therapy (P = .03) and mechanical ventilation (P < .001), as well as a higher probability of requiring mechanical ventilation (P = .001) and of ICU admission (P = .003) compared with children with normal weight. Patients with overweight presented more days of mechanical ventilation (P < .001) than patients with normal weight. No significant differences were found between the presence of viral coinfection and nutritional status. CONCLUSION Overnutrition is associated with greater severity of viral respiratory infection in hospitalized children.
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Affiliation(s)
- Camila Cáceres
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Macarena Castillo
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Karin Carrillo
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | | | | | - César Maquilón
- Unidad Broncopulmonar Adulto, Clínica Dávila, Santiago, Chile
| | - Daniela Toro-Ascuy
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | | | - Loreto F Fuenzalida
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile.
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10
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Abu-Raya B, Viñeta Paramo M, Reicherz F, Lavoie PM. Why has the epidemiology of RSV changed during the COVID-19 pandemic? EClinicalMedicine 2023; 61:102089. [PMID: 37483545 PMCID: PMC10359735 DOI: 10.1016/j.eclinm.2023.102089] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has drastically perturbed the epidemiology of Respiratory Syncytial Virus (RSV) respiratory tract infections in children. The reasons for this are not clear. In this article, we review the current literature and critically discuss the different theories to explain why the epidemiology of RSV has changed during the COVID-19 pandemic. Proposed mechanisms include decreased viral immunity in vulnerable age groups caused by the prolonged lack of RSV circulation early in the pandemic, potential Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2)-induced immune dysregulation, viral interactions between SARS-CoV-2 and RSV, and modifications in health-seeking behaviors as well as heath systems factors. Research in viral genomics and phylogeny, and more robust immunology research is needed to guide RSV prevention and health care resource planning.
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Affiliation(s)
- Bahaa Abu-Raya
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - Marina Viñeta Paramo
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - Frederic Reicherz
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - Pascal Michel Lavoie
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, Canada
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11
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Schuster JE, Erickson TR, Goldman JL, Benjamin DK, Brookhart MA, Dewhurst S, Fist A, Foxe J, Godambe M, Gwynn L, Kiene SM, Keener Mast D, McDaniels-Davidson C, Newland JG, Oren E, Selvarangan R, Shinde N, Walsh T, Watterson T, Zand M, Zimmerman KO, Kalu IC. Utilization and Impact of Symptomatic and Exposure SARS-CoV-2 Testing in K-12 Schools. Pediatrics 2023; 152:e2022060352I. [PMID: 37394504 PMCID: PMC10312273 DOI: 10.1542/peds.2022-060352i] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 07/04/2023] Open
Abstract
OBJECTIVES The Centers for Disease Control and Prevention recommend that schools can offer severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic (on-demand) testing for students and staff with coronavirus disease 2019 symptoms or exposures. Data related to the uptake, implementation, and effect of school-associated on-demand diagnostic testing have not been described. METHODS The Rapid Acceleration of Diagnostics Underserved Populations Return to School program provided resources to researchers to implement on-demand SARS-CoV-2 testing in schools. This study describes the strategies used and uptake among the different testing programs. Risk of positivity was compared for symptomatic and exposure testing during the δ and ο variant periods. We estimated the number of school absence days saved with school-based diagnostic testing. RESULTS Of the 16 eligible programs, 7 provided school-based on-demand testing. The number of persons that participated in these testing programs is 8281, with 4134 (49.9%) receiving >1 test during the school year. Risk of positivity was higher for symptomatic testing compared with exposure testing and higher during the ο variant predominant period compared with the δ variant predominant period. Overall, access to testing saved an estimated 13 806 absent school days. CONCLUSIONS School-based on-demand SARS-CoV-2 testing was used throughout the school year, and nearly half the participants accessed testing on more than 1 occasion. Future studies should work to understand participant preferences around school-based testing and how these strategies can be used both during and outside of pandemics.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maya Godambe
- Division of Pediatric Infectious Diseases, Washington University in St Louis, St Louis, Missouri
| | - Lisa Gwynn
- Department of Pediatrics, Miller School of Medicine, University of Miami, Miami, Florida
| | - Susan M. Kiene
- Division of Epidemiology and Biostatistics, School of Public Health, San Diego State University, San Diego, California
| | | | - Corinne McDaniels-Davidson
- Division of Epidemiology and Biostatistics, School of Public Health, San Diego State University, San Diego, California
| | - Jason G. Newland
- Division of Pediatric Infectious Diseases, Washington University in St Louis, St Louis, Missouri
| | - Eyal Oren
- Division of Epidemiology and Biostatistics, School of Public Health, San Diego State University, San Diego, California
| | - Rangaraj Selvarangan
- Pathology and Laboratory Medicine, Children’s Mercy Kansas City, University of Missouri-Kansas City, Kansas City, Missouri
| | - Nidhi Shinde
- Division of Pediatric Infectious Diseases, Washington University in St Louis, St Louis, Missouri
| | - Tyler Walsh
- Division of Pediatric Infectious Diseases, Washington University in St Louis, St Louis, Missouri
| | - Treymayne Watterson
- Division of Pediatric Infectious Diseases, Washington University in St Louis, St Louis, Missouri
| | - Martin Zand
- Division of Nephrology, School of Medicine and Dentistry, University of Rochester, Rochester, New York
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12
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Alotaibi BS, Tantry BA, Bandy A, Ahmad R, Khursheed SQ, Ahmad A, Hakami MA, Shah NN. Simultaneous Detection of Influenza A/B, Respiratory Syncytial Virus, and SARS-CoV-2 in Nasopharyngeal Swabs by One-Tube Multiplex Reverse Transcription Polymerase Chain Reaction. Trop Med Infect Dis 2023; 8:326. [PMID: 37368744 DOI: 10.3390/tropicalmed8060326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The treatment and outcome of respiratory virus infections differ. SARS-CoV-2, as well as other respiratory viruses such as influenza virus (A and B) and respiratory syncytial virus (RSV), require simultaneous, cost-effective, and rapid differential detection. We used a gold standard five-target single-step RT-PCR to detect influenza viruses, RSV, and SARS-CoV-2, and this method can be extended to detect influenza virus subtypes. As a result, this five-target single-step RT-PCR method is ideal for differentiating respiratory viruses. The 5' nuclease activity of Taq DNA polymerase is used in the real-time reverse transcription PCR assay. The Taq man fast viral 1-step enzyme is a 4× Master mix and five-target primer probe mix that detects influenza A, influenza B, SARS-CoV-2 ORF1ab, respiratory syncytial viruses A/B and actin. When compared with TaqMan TM and Invitrogen superscript TM III Platinum and the Meril Kit for SARS-CoV-2, the assay demonstrated 100% sensitivity, specificity, and amplification efficiency of 90.1% for target genes. In conclusion, our one-tube multiplex RT-PCR assay offers a rapid and reliable method for the simultaneous detection of influenza A/B, RSV, and SARS-CoV-2 from nasopharyngeal swabs. This assay has the potential to enhance diagnostic capabilities and improve public health responses during respiratory outbreaks, enabling timely interventions and informed decision making.
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Affiliation(s)
- Bader S Alotaibi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 19257, Saudi Arabia
| | - Bilal Ahmad Tantry
- Department of Microbiology, Government Medical College, Srinagar 190010, India
| | - Altaf Bandy
- Department of Community Medicine, College of Medicine, Shaqra University, Shaqra 15273, Saudi Arabia
| | - Reyaz Ahmad
- Department of Microbiology, Government Medical College, Srinagar 190010, India
| | | | - Arshid Ahmad
- Department of Pulmonary Medicine, Government Medical College, Srinagar 190001, India
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Shaqra University, Alquwayiyah 19257, Saudi Arabia
| | - Naveed Nazir Shah
- Department of Pulmonary Medicine, Government Medical College, Srinagar 190001, India
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13
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Weidmann MD, Green DA, Berry GJ, Wu F. Assessing respiratory viral exclusion and affinity interactions through co-infection incidence in a pediatric population during the 2022 resurgence of influenza and RSV. Front Cell Infect Microbiol 2023; 13:1208235. [PMID: 37389220 PMCID: PMC10302716 DOI: 10.3389/fcimb.2023.1208235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction In the Northeast US, respiratory viruses such as influenza and respiratory syncytial virus (RSV), which were largely suppressed by COVID-19-related social distancing, made an unprecedented resurgence during 2022, leading to a substantial rise in viral co-infections. However, the relative rates of co-infection with seasonal respiratory viruses over this period have not been assessed. Methods Here we reviewed multiplex respiratory viral PCR data (BioFire FilmArray™ Respiratory Panel v2.1 [RPP]) from patients with respiratory symptoms presenting to our medical center in New York City to assess co-infection rates of respiratory viruses, which were baselined to total rates of infection for each virus. We examined trends in monthly RPP data from adults and children during November 2021 through December 2022 to capture the full seasonal dynamics of respiratory viruses across periods of low and high prevalence. Results Of 50,022 RPPs performed for 34,610 patients, 44% were positive for at least one target, and 67% of these were from children. The overwhelming majority of co-infections (93%) were seen among children, for whom 21% of positive RPPs had two or more viruses detected, as compared to just 4% in adults. Relative to children for whom RPPs were ordered, children with co-infections were younger (3.0 vs 4.5 years) and more likely to be seen in the ED or outpatient settings than inpatient and ICU settings. In children, most viral co-infections were found at significantly reduced rates relative to that expected from the incidence of each virus, especially those involving SARS-CoV-2 and influenza. SARS-CoV-2 positive children had an 85%, 65% and 58% reduced rate of co-infection with influenza, RSV, and Rhino/enteroviruses, respectively, after compensating for the incidence of infection with each virus (p< 0.001). Discussion Our results demonstrate that most respiratory viruses peaked in different months and present in co-infections less than would be expected based on overall rates of infection, suggesting a viral exclusionary effect between most seasonal respiratory viruses, including SARS-CoV-2, influenza and RSV. We also demonstrate the significant burden of respiratory viral co-infections among children. Further work is necessary to understand what predisposes certain patients for viral co-infection despite this exclusionary effect.
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Affiliation(s)
| | | | | | - Fann Wu
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
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14
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Maltezou HC, Papanikolopoulou A, Vassiliu S, Theodoridou K, Nikolopoulou G, Sipsas NV. COVID-19 and Respiratory Virus Co-Infections: A Systematic Review of the Literature. Viruses 2023; 15:865. [PMID: 37112844 PMCID: PMC10142898 DOI: 10.3390/v15040865] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
Τhe COVID-19 pandemic highly impacted the circulation, seasonality, and morbidity burden of several respiratory viruses. We reviewed published cases of SARS-CoV-2 and respiratory virus co-infections as of 12 April 2022. SARS-CoV-2 and influenza co-infections were reported almost exclusively during the first pandemic wave. It is possible that the overall incidence of SARS-CoV-2 co-infections is higher because of the paucity of co-testing for respiratory viruses during the first pandemic waves when mild cases might have been missed. Animal models indicate severe lung pathology and high fatality; nevertheless, the available literature is largely inconclusive regarding the clinical course and prognosis of co-infected patients. Animal models also indicate the importance of considering the sequence timing of each respiratory virus infection; however, there is no such information in reported human cases. Given the differences between 2020 and 2023 in terms of epidemiology and availability of vaccines and specific treatment against COVID-19, it is rational not to extrapolate these early findings to present times. It is expected that the characteristics of SARS-CoV-2 and respiratory virus co-infections will evolve in the upcoming seasons. Multiplex real-time PCR-based assays have been developed in the past two years and should be used to increase diagnostic and infection control capacity, and also for surveillance purposes. Given that COVID-19 and influenza share the same high-risk groups, it is essential that the latter get vaccinated against both viruses. Further studies are needed to elucidate how SARS-CoV-2 and respiratory virus co-infections will be shaped in the upcoming years, in terms of impact and prognosis.
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Affiliation(s)
- Helena C. Maltezou
- Directorate of Research, Studies and Documentation, National Public Health Organization, 15123 Athens, Greece
| | - Amalia Papanikolopoulou
- Third Department of Internal Medicine, Sotiria General Hospital for Thoracic Diseases, National and Kapodistrian University of Athens, School of Medicine, Sotiria General Hospital, 11527 Athens, Greece
| | | | - Kalliopi Theodoridou
- Department of Microbiology, Andreas Sygros Hospital, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Georgia Nikolopoulou
- Department of Hepatitides, National Public Health Organization, 15123 Athens, Greece
| | - Nikolaos V. Sipsas
- Pathophysiology Department, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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15
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Fall A, Forman M, Morris CP, Gniazdowski V, Luo CH, Hanlon A, Miller H, Bergman Y, Mostafa HH. Enterovirus characterized from cerebrospinal fluid in a cohort from the Eastern United States. J Clin Virol 2023; 161:105401. [PMID: 36805602 DOI: 10.1016/j.jcv.2023.105401] [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: 09/19/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Enteroviruses (EVs) are predominant causes of a spectrum of neurological diseases. To better understand the origins of the outbreaks of disease associated with EV, it is essential to develop an efficient surveillance system that identifies the circulating EVs and correlate their genomic evolution with the disease presentations. METHODS The clinical presentations of patients with positive EV from cerebrospinal fluid (CSF) between 2014 and 2022, diagnosed at the Johns Hopkins Medical Microbiology Laboratory, were compared from year to year. EV typing and whole genome sequencing were performed and correlated to the spectrum of disease. RESULTS A total of 95 CSF specimens were positive for EV between 2014 and 2022. The percentage positivity ranged from the lowest of 1.1% in 2020 to the highest of 3.2% in 2015. The median ages declined from 22 years in 2014 to less than one year starting in 2016 to 34 in 2022. Typing using VP1 sequencing revealed that E30 and E6 were associated with meningitis in adults but coxsackieviruses (CVs-B3 and B5) were detected from pediatric patients with fever. Whole genome sequencing revealed multiple recombination events. In 2020, a recombinant CV-A9 was detected in a CSF sample associated with unusual presentation of sepsis, profound acute bilateral sensory neural hearing loss, and myofasciitis. CONCLUSIONS EV genomic surveillance is needed for a better understanding of the genetic determinants of neurovirulence. Whole genome sequencing can reveal recombination events missed by traditional molecular surveillance methods.
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Affiliation(s)
- Amary Fall
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Michael Forman
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - C Paul Morris
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA; National Institute of Allergy and Infectious Disease, National Institutes of Health, Frederick, MD, USA
| | - Victoria Gniazdowski
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Chun Huai Luo
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Ann Hanlon
- Johns Hopkins Hospital Medical Microbiology Laboratory, Meyer B-130, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Heather Miller
- Johns Hopkins Hospital Medical Microbiology Laboratory, Meyer B-130, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Yehudit Bergman
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA
| | - Heba H Mostafa
- Johns Hopkins School of Medicine, Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD, 21287-7093, USA.
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16
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Chuang YC, Lin KP, Wang LA, Yeh TK, Liu PY. The Impact of the COVID-19 Pandemic on Respiratory Syncytial Virus Infection: A Narrative Review. Infect Drug Resist 2023; 16:661-675. [PMID: 36743336 PMCID: PMC9897071 DOI: 10.2147/idr.s396434] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/12/2023] [Indexed: 02/01/2023] Open
Abstract
Respiratory syncytial virus (RSV) is one of the most common respiratory viruses. It not only affects young children but also the elderly and immunocompromised patients. After the emergence of SARS-CoV-2 and the corona virus disease 2019 (COVID-19) era, a dramatic reduction in RSV activity was found, which coincided with the implementation of public health and social measures (PHSMs). However, the correlation is more complicated than we initially thought. After PHSMs were gradually lifted, a seasonality shift and a delayed RSV outbreak with greater number of infected patients were found in numerous countries, such as Israel, Australia, South Africa, New Zealand, France, United States, and Japan. Several hypotheses and possible reasons explaining the interaction between SARS-CoV-2 and RSV were mentioned. Since RSV vaccinations are still under investigation, administration of palivizumab should be considered in high-risk patients. In the post-COVID-19 era, greater attention should be paid to a further resurgence of RSV. In this narrative review, we conducted a thorough review of the current knowledge on the epidemiology of RSV during the COVID-19 era, the out-of-season outbreak of RSV, and the data on co-infection with RSV and SARS-CoV-2.
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Affiliation(s)
- Yu-Chuan Chuang
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Kuan-Pei Lin
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Li-An Wang
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ting-Kuang Yeh
- Division of Infectious Disease, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Division of Infectious Disease, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan,Ph.D. in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan,Correspondence: Po-Yu Liu, Division of Infectious Disease, Department of Internal Medicine, Taichung Veterans General Hospital, No. 1650, Sec. 4, Taiwan Blvd., Xitun Dist, Taichung City, 407219, Taiwan, Tel +886 4 2359 2525, Email
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17
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Hansen C, Perofsky AC, Burstein R, Famulare M, Boyle S, Prentice R, Marshall C, McCormick BJJ, Reinhart D, Capodanno B, Truong M, Schwabe-Fry K, Kuchta K, Pfau B, Acker Z, Lee J, Sibley TR, McDermot E, Rodriguez-Salas L, Stone J, Gamboa L, Han PD, Duchin JS, Waghmare A, Englund JA, Shendure J, Bedford T, Chu HY, Starita LM, Viboud C. Trends in Risk Factors and Symptoms Associated With SARS-CoV-2 and Rhinovirus Test Positivity in King County, Washington, June 2020 to July 2022. JAMA Netw Open 2022; 5:e2245861. [PMID: 36484987 PMCID: PMC9856230 DOI: 10.1001/jamanetworkopen.2022.45861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
IMPORTANCE Few US studies have reexamined risk factors for SARS-CoV-2 positivity in the context of widespread vaccination and new variants or considered risk factors for cocirculating endemic viruses, such as rhinovirus. OBJECTIVES To evaluate how risk factors and symptoms associated with SARS-CoV-2 test positivity changed over the course of the pandemic and to compare these with the risk factors associated with rhinovirus test positivity. DESIGN, SETTING, AND PARTICIPANTS This case-control study used a test-negative design with multivariable logistic regression to assess associations between SARS-CoV-2 and rhinovirus test positivity and self-reported demographic and symptom variables over a 25-month period. The study was conducted among symptomatic individuals of all ages enrolled in a cross-sectional community surveillance study in King County, Washington, from June 2020 to July 2022. EXPOSURES Self-reported data for 15 demographic and health behavior variables and 16 symptoms. MAIN OUTCOMES AND MEASURES Reverse transcription-polymerase chain reaction-confirmed SARS-CoV-2 or rhinovirus infection. RESULTS Analyses included data from 23 498 individuals. The median (IQR) age of participants was 34.33 (22.42-45.08) years, 13 878 (59.06%) were female, 4018 (17.10%) identified as Asian, 654 (2.78%) identified as Black, and 2193 (9.33%) identified as Hispanic. Close contact with an individual with SARS-CoV-2 (adjusted odds ratio [aOR], 3.89; 95% CI, 3.34-4.57) and loss of smell or taste (aOR, 3.49; 95% CI, 2.77-4.41) were the variables most associated with SARS-CoV-2 test positivity, but both attenuated during the Omicron period. Contact with a vaccinated individual with SARS-CoV-2 (aOR, 2.03; 95% CI, 1.56-2.79) was associated with lower odds of testing positive than contact with an unvaccinated individual with SARS-CoV-2 (aOR, 4.04; 95% CI, 2.39-7.23). Sore throat was associated with Omicron infection (aOR, 2.27; 95% CI, 1.68-3.20) but not Delta infection. Vaccine effectiveness for participants fully vaccinated with a booster dose was 93% (95% CI, 73%-100%) for Delta, but not significant for Omicron. Variables associated with rhinovirus test positivity included being younger than 12 years (aOR, 3.92; 95% CI, 3.42-4.51) and experiencing a runny or stuffy nose (aOR, 4.58; 95% CI, 4.07-5.21). Black race, residing in south King County, and households with 5 or more people were significantly associated with both SARS-CoV-2 and rhinovirus test positivity. CONCLUSIONS AND RELEVANCE In this case-control study of 23 498 symptomatic individuals, estimated risk factors and symptoms associated with SARS-CoV-2 infection changed over time. There was a shift in reported symptoms between the Delta and Omicron variants as well as reductions in the protection provided by vaccines. Racial and sociodemographic disparities persisted in the third year of SARS-CoV-2 circulation and were also present in rhinovirus infection. Trends in testing behavior and availability may influence these results.
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Affiliation(s)
- Chelsea Hansen
- Brotman Baty Institute, University of Washington, Seattle
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Amanda C. Perofsky
- Brotman Baty Institute, University of Washington, Seattle
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Roy Burstein
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Michael Famulare
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shanda Boyle
- Brotman Baty Institute, University of Washington, Seattle
| | - Robin Prentice
- Brotman Baty Institute, University of Washington, Seattle
| | | | | | - David Reinhart
- Brotman Baty Institute, University of Washington, Seattle
| | - Ben Capodanno
- Brotman Baty Institute, University of Washington, Seattle
| | - Melissa Truong
- Brotman Baty Institute, University of Washington, Seattle
| | | | - Kayla Kuchta
- Brotman Baty Institute, University of Washington, Seattle
| | - Brian Pfau
- Brotman Baty Institute, University of Washington, Seattle
| | - Zack Acker
- Brotman Baty Institute, University of Washington, Seattle
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Evan McDermot
- Brotman Baty Institute, University of Washington, Seattle
| | | | - Jeremy Stone
- Brotman Baty Institute, University of Washington, Seattle
| | - Luis Gamboa
- Brotman Baty Institute, University of Washington, Seattle
| | - Peter D. Han
- Brotman Baty Institute, University of Washington, Seattle
- Department of Genome Sciences, University of Washington, Seattle
| | - Jeffery S. Duchin
- Public Health Seattle and King County, Seattle, Washington
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- School of Public Health, University of Washington, Seattle
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Seattle Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle
| | - Janet A. Englund
- Brotman Baty Institute, University of Washington, Seattle
- Seattle Children’s Research Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle
| | - Jay Shendure
- Brotman Baty Institute, University of Washington, Seattle
- Department of Genome Sciences, University of Washington, Seattle
- Howard Hughes Medical Institute, Seattle, Washington
| | - Trevor Bedford
- Brotman Baty Institute, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
- Howard Hughes Medical Institute, Seattle, Washington
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Lea M. Starita
- Brotman Baty Institute, University of Washington, Seattle
- Department of Genome Sciences, University of Washington, Seattle
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland
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18
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Weidmann MD, Berry GJ, Green DA, Wu F. Prevalence and clinical disease severity of respiratory co-infections during the COVID-19 pandemic. ADVANCES IN MOLECULAR PATHOLOGY 2022. [PMCID: PMC9364747 DOI: 10.1016/j.yamp.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Impact of COVID-19 on the Changing Patterns of Respiratory Syncytial Virus Infections. Infect Dis Rep 2022; 14:558-568. [PMID: 35893478 PMCID: PMC9394296 DOI: 10.3390/idr14040059] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
Seasonal epidemics of respiratory syncytial virus (RSV) is one of the leading causes of hospitalization and mortality among children. Preventive measures implemented to reduce the spread of SARS-CoV-2, including facemasks, stay-at-home orders, closure of schools and local-national borders, and hand hygiene, may have also prevented the transmission of RSV and influenza. However, with the easing of COVID-19 imposed restrictions, many regions are noticing a delayed RSV outbreak. Some of these regions have also noted an increase in severity of these delayed RSV outbreaks partly due to a lack of protective immunity in the community following a lack of exposure from the previous season. Lessons learned from the COVID-19 pandemic can be implemented for controlling RSV outbreaks, including: (1) measures to reduce the spread, (2) effective vaccine development, and (3) genomic surveillance tools and computational modeling to predict the timing and severity of RSV outbreaks. These measures can help reduce the severity and prepare the health care system to deal with future RSV outbreaks by appropriate and timely allocation of health care resources.
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20
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Fall A, Gallagher N, Morris CP, Norton JM, Pekosz A, Klein E, Mostafa HH. Circulation of Enterovirus D68 during Period of Increased Influenza-Like Illness, Maryland, USA, 2021. Emerg Infect Dis 2022; 28:1525-1527. [PMID: 35642471 PMCID: PMC9239864 DOI: 10.3201/eid2807.212603] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report enterovirus D68 circulation in Maryland, USA, during September-October 2021, which was associated with a spike in influenza-like illness. The characterized enterovirus D68 genomes clustered within the B3 subclade that circulated in 2018 in Europe and the United States.
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21
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Chan KKP, Hui DSC. Contemporary Concise Review 2021: COVID-19 and other respiratory infections. Respirology 2022; 27:661-668. [PMID: 35670259 PMCID: PMC9347613 DOI: 10.1111/resp.14305] [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: 05/04/2022] [Accepted: 05/12/2022] [Indexed: 12/15/2022]
Abstract
Bats are likely the primary source of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Minks are highly susceptible to infection by SARS‐CoV‐2. Transmission from asymptomatic individuals was estimated to account for over 50% of all transmissions of coronavirus disease 2019 (COVID‐19) cases. SARS‐CoV‐2 is evolving towards more efficient aerosol transmission. Remdesivir, baricitinib, tocilizumab and dexamethasone are frequently used for the treatment of patients with respiratory failure due to COVID‐19. There is a rising incidence of non‐tuberculous Mycobacterium pulmonary disease globally, with a higher prevalence in Asian countries than in the Western world. Protracted bacterial bronchitis is a common cause of chronic productive cough in childhood. Re‐emergence of respiratory syncytial virus may occur after the relaxation of infection control measures and the reopening of borders during COVID‐19 pandemic.
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Affiliation(s)
- Ken K P Chan
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong
| | - David S C Hui
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong.,Stanley Ho Center for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong
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22
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Lu J, Wu T, Zeng Q, Chen Y, Liu Y, Wu D. Epidemiology of rhinovirus under the COVID‐19 pandemic in Guangzhou, China, 2020. Immun Inflamm Dis 2022; 10:e632. [PMID: 35634957 PMCID: PMC9092004 DOI: 10.1002/iid3.632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/07/2022] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Methods Results Conclusion
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Affiliation(s)
- Jianyun Lu
- Director Guangzhou Baiyun District Center for Disease Control and Prevention Guangzhou Guangdong P. R. China
| | - Tiantian Wu
- Institute of Human Virology
- Zhongshan School of Medicine
- Key Laboratory of Tropical Disease Control of Ministry of Education Sun Yat‐sen University Guangzhou P. R. China
| | - Qing Zeng
- Department of Biostatistics and Cancer Registration Guangzhou Center for Disease Control and Prevention Guangzhou P. R. China
| | - Yiyun Chen
- Department of Biostatistics and Cancer Registration Guangzhou Center for Disease Control and Prevention Guangzhou P. R. China
| | - Yanhui Liu
- Department of Biostatistics and Cancer Registration Guangzhou Center for Disease Control and Prevention Guangzhou P. R. China
| | - Di Wu
- Department of Biostatistics and Cancer Registration Guangzhou Center for Disease Control and Prevention Guangzhou P. R. China
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23
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Fall A, Eldesouki RE, Sachithanandham J, Paul Morris C, Norton JM, Gaston DC, Forman M, Abdullah O, Gallagher N, Li M, Swanson NJ, Pekosz A, Klein EY, Mostafa HH. A Quick Displacement of the SARS-CoV-2 variant Delta with Omicron: Unprecedented Spike in COVID-19 Cases Associated with Fewer Admissions and Comparable Upper Respiratory Viral Loads. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022. [PMID: 35118480 PMCID: PMC8811948 DOI: 10.1101/2022.01.26.22269927] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The increase in SARS-CoV-2 infections in December 2021 in the United States was driven primarily by the Omicron variant which largely displaced the Delta over a three week span. Outcomes from infection with the Omicron remain uncertain. We evaluate whether clinical outcomes and viral loads differ between Delta and Omicron infections during the period when both variants were co-circulating. METHODS Remnant clinical specimens from patients that tested positive for SARS-CoV-2 after standard of care testing between the last week of November and the end of December 2021were used for whole viral genome sequencing. Cycle threshold values (Ct) for viral RNA, the presence of infectious virus, and levels of respiratory IgG were measured, and clinical outcomes were obtained. Differences in each measure were compared between variants stratified by vaccination status. RESULTS The Omicron variant displaced the Delta during the study period and constituted 95% of the circulating lineages by the end of December 2021. Patients with Omicron infections (N= 1121) were more likely to be vaccinated compared to patients with Delta (N = 910), but were less likely to be admitted, require ICU level care, or succumb to infection regardless of vaccination status. There was no significant difference in Ct values based on the lineage regardless of the vaccination status. Recovery of infectious virus in cell culture was reduced in boosted patients compared to fully vaccinated without a booster and unvaccinated when infected with the Delta lineage. However, in patients with Omicron infections, recovery of infectious virus was not affected by vaccination. CONCLUSIONS Omicron infections of vaccinated individuals are expected, yet admissions are less frequent. Admitted patients might develop severe disease comparable to Delta. Efforts for reducing the Omicron transmission are required as even though the admission risk is lower, the numbers of infections continue to be high. RESEARCH IN CONTEXT EVIDENCE BEFORE THIS STUDY The unprecedented increase in COVID-19 cases in the month of December 2021, associated with the displacement of the Delta variant with the Omicron, triggered a lot of concerns. An understanding of the disease severity associated with infections with Omicron is essential as well as the virological determinants that contributed to its widespread predominance. We searched PubMed for articles published up to January 23, 2022, using the search terms ("Omicron") AND ("Disease severity") as well as ("Omicron") AND ("Viral load") And/ or ("Cell culture"). Our search yielded 3 main studies that directly assessed the omicron's clinical severity in South Africa, its infectious viral load compared to Delta, and the dynamics of viral RNA shedding. In South Africa, compared to Delta, Omicron infected patients showed a significant reduction in severe disease. In this study, Omicron and non-Omicron variants were characterized based on S gene target failure using the TaqPath COVID-19 PCR (Thermo Fisher Scientific). In the study from Switzerland that assessed the infectious viral load in Omicron versus Delta, the authors analyzed only 18 Omicron samples that were all from vaccinated individuals to show that compared to Delta, Omicron had equivalent infectious viral titers. The third study that assessed the Omicron viral dynamics showed that the peak viral RNA in Omicron infections is lower than Delta. No published studies assessed the clinical discrepancies of Omicron and Delta infected patients from the US, nor comprehensively assessed, by viral load and cell culture studies, the characteristics of both variants stratified by vaccination status. ADDED VALUE OF THIS STUDY To the best of our knowledge, this is the only study to date to compare the clinical characteristics and outcomes after infection with the Omicron variant compared to Delta in the US using variants characterized by whole genome sequencing and a selective time frame when both variant co-circulated. It is also the first study to stratify the analysis based on the vaccination status and to compare fully vaccinated patients who didn't receive a booster vaccination to patients who received a booster vaccination. In addition, we provide a unique viral RNA and infectious virus load analyses to compare Delta and Omicron samples from unvaccinated, fully vaccinated, and patients with booster vaccination. IMPLICATIONS OF ALL THE AVAILABLE EVIDENCE Omicron associated with a significant increase in infections in fully and booster vaccinated individuals but with less admissions and ICU level care. Admitted patients showed similar requirements for supplemental oxygen and ICU level care when compared to Delta admitted patients. Viral loads were similar in samples from Omicron and Delta infected patients regardless of the vaccination status. The recovery of infectious virus on cell culture was reduced in samples from patients infected with Delta who received a booster dose, but this was not the case with Omicron. The recovery of infectious virus was equivalent in Omicron infected unvaccinated, fully vaccinated, and samples from patients who received booster vaccination. FUNDING NIH/NIAID Center of Excellence in Influenza Research and Surveillance contract HHS N2772201400007C, Johns Hopkins University, Maryland department of health, Centers for Disease Control and Prevention contract 75D30121C11061.
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