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Trifonova I, Korsun N, Madzharova I, Alexiev I, Ivanov I, Levterova V, Grigorova L, Stoikov I, Donchev D, Christova I. Epidemiological and Genetic Characteristics of Respiratory Viral Coinfections with Different Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Viruses 2024; 16:958. [PMID: 38932250 PMCID: PMC11209099 DOI: 10.3390/v16060958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
This study aimed to determine the incidence and etiological, seasonal, and genetic characteristics of respiratory viral coinfections involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between October 2020 and January 2024, nasopharyngeal samples were collected from 2277 SARS-CoV-2-positive patients. Two multiplex approaches were used to detect and sequence SARS-CoV-2, influenza A/B viruses, and other seasonal respiratory viruses: multiplex real-time polymerase chain reaction (PCR) and multiplex next-generation sequencing. Coinfections of SARS-CoV-2 with other respiratory viruses were detected in 164 (7.2%) patients. The most common co-infecting virus was respiratory syncytial virus (RSV) (38 cases, 1.7%), followed by bocavirus (BoV) (1.2%) and rhinovirus (RV) (1.1%). Patients ≤ 16 years of age had the highest rate (15%) of mixed infections. Whole-genome sequencing produced 19 complete genomes of seasonal respiratory viral co-pathogens, which were subjected to phylogenetic and amino acid analyses. The detected influenza viruses were classified into the genetic groups 6B.1A.5a.2a and 6B.1A.5a.2a.1 for A(H1N1)pdm09, 3C.2a1b.2a.2a.1 and 3C.2a.2b for A(H3N2), and V1A.3a.2 for the B/Victoria lineage. The RSV-B sequences belonged to the genetic group GB5.0.5a, with HAdV-C belonging to type 1, BoV to genotype VP1, and PIV3 to lineage 1a(i). Multiple amino acid substitutions were identified, including at the antibody-binding sites. This study provides insights into respiratory viral coinfections involving SARS-CoV-2 and reinforces the importance of genetic characterization of co-pathogens in the development of therapeutic and preventive strategies.
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Affiliation(s)
- Ivelina Trifonova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Neli Korsun
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Iveta Madzharova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivailo Alexiev
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivan Ivanov
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Viktoria Levterova
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Lyubomira Grigorova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivan Stoikov
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Dean Donchev
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Iva Christova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
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Trifonova I, Korsun N, Madzharova I, Velikov P, Alexsiev I, Grigorova L, Voleva S, Yordanova R, Ivanov I, Tcherveniakova T, Christova I. Prevalence and clinical impact of mono- and co-infections with endemic coronaviruses 229E, OC43, NL63, and HKU-1 during the COVID-19 pandemic. Heliyon 2024; 10:e29258. [PMID: 38623185 PMCID: PMC11016702 DOI: 10.1016/j.heliyon.2024.e29258] [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: 10/05/2023] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
Introduction Endemic human coronaviruses (eHCoVs) are found worldwide and usually result in mild to moderate upper respiratory tract infections. They can lead to more severe illnesses such as croup, bronchiolitis, and pneumonia in vulnerable populations. During the coronavirus disease 2019 (COVID-19) pandemic, information on HCoV prevalence and incidence and clinical impact of co-infections of HCoV with SARS-CoV-2 was lacking. Objectives Thus, this study aimed to determine the prevalence and clinical significance of infections caused by eHCoVs during the COVID-19 pandemic in Bulgaria. Methods From January 2021 to December 2022, nasopharyngeal swabs of patients with acute upper or lower respiratory tract infections were tested for 17 respiratory viruses using multiplex real-time polymerase chain reaction assays. The clinical data and laboratory parameters of patients infected with respiratory viruses were analysed. Results Of the 1375 patients screened, 24 (1.7 %) were positive for HCoVs, and 197 (14.3 %) were positive for eight other seasonal respiratory viruses. Five (0.7 %) of 740 patients positive for SARS-CoV-2 were co-infected with eHCoVs. Co-infected patients had a mean C-reactive protein level of 198.5 ± 2.12 mg/mL and a mean oxygen saturation of 82 ± 2.8 mmHg, while those in patients co-infected with SARS-CoV-2 and other respiratory viruses were 61.8 mg/mL and 92.8 ± 4.6 mmHg, respectively (p < 0.05). Pneumonia was diagnosed in 63.3 % of patients with HCoV infection and 6 % of patients positive for other seasonal respiratory viruses (p < 0.05). Patients with SARS-CoV-2 mono-infection stayed in hospital for an average of 5.8 ± 3.7 days, whereas the average hospital stay of patients with eHCoV and SARS-CoV-2 co-infection was 9 ± 1.4 days (p < 0.05). Conclusion These findings indicate the low prevalence of eHCoVs and low co-infection rate between eHCoVs and SARS-CoV-2 during the COVID-19 pandemic in Bulgaria. Despite their low incidence, such mixed infections can cause severe signs that require oxygen therapy and longer hospital stays, underlining the need for targeted testing of severe COVID-19 cases to identify potential co-infections.
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Affiliation(s)
- I. Trifonova
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - N. Korsun
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - I. Madzharova
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - P. Velikov
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - I. Alexsiev
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - L. Grigorova
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
| | - S. Voleva
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - R. Yordanova
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - I. Ivanov
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - T. Tcherveniakova
- Infectious Disease Hospital “Prof. Ivan Kirov”, Department for Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Bulgaria
| | - I. Christova
- National Laboratory “Influenza and ARD”, Department of Virology, National Center of Infectious and Parasitic Diseases (NCIPD), Sofia, Bulgaria
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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: 22] [Impact Index Per Article: 22.0] [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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Krumbein H, Kümmel LS, Fragkou PC, Thölken C, Hünerbein BL, Reiter R, Papathanasiou KA, Renz H, Skevaki C. Respiratory viral co-infections in patients with COVID-19 and associated outcomes: A systematic review and meta-analysis. Rev Med Virol 2023; 33:e2365. [PMID: 35686619 PMCID: PMC9347814 DOI: 10.1002/rmv.2365] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 01/28/2023]
Abstract
The aim of this systematic review and meta-analysis was to critically assess the published literature related to community-acquired viral co-infections and COVID-19 and to evaluate the prevalence, most identified co-pathogens, and relevant risk factors. Furthermore, we aimed to examine the clinical features and outcomes of co-infected compared to mono-infected COVID-19 patients. We systematically searched PubMed, Web of Science, Embase, Scopus, and The Cochrane Library for studies published from 1 November 2019 to 13 August 2021. We included patients of all ages and any COVID-19 severity who were screened for respiratory viral co-infection within 48 h of COVID-19 diagnosis. The main outcome was the proportion of patients with a respiratory viral co-infection. The systematic review was registered to PROSPERO (CRD42021272235). Out of 6053 initially retrieved studies, 59 studies with a total of 16,643 SARS-CoV-2 positive patients were included. The global pooled prevalence was 5.01% (95% CI 3.34%-7.27%; I2 = 95%) based on a random-effects model, with Influenza Viruses (1.54%) and Enteroviruses (1.32%) being the most prevalent pathogens. Subgroup analyses showed that co-infection was significantly higher in paediatric (9.39%) than adult (3.51%) patients (p-value = 0.02). Furthermore, co-infected patients were more likely to be dyspnoeic and the odds of fatality (OR = 1.66) were increased. Although a relatively low proportion of COVID-19 patients have a respiratory viral co-infection, our findings show that multiplex viral panel testing may be advisable in patients with compatible symptoms. Indeed, respiratory virus co-infections may be associated with adverse clinical outcomes and therefore have therapeutic and prognostic implications.
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Affiliation(s)
- Hanna Krumbein
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | - Lara S. Kümmel
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | - Paraskevi C. Fragkou
- Fourth Department of Internal MedicineMedical School of AthensNational and Kapodistrian University of AthensAttikon University HospitalAthensGreece
| | - Clemens Thölken
- Institute of Medical Bioinformatics and BiostatisticsMedical FacultyPhilipps University of MarburgMarburgGermany
| | - Ben L. Hünerbein
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | - Rieke Reiter
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | | | - Harald Renz
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
| | - Chrysanthi Skevaki
- Institute of Laboratory MedicineUniversities of Giessen and Marburg Lung Center (UGMLC)Philipps Universität MarburgGerman Center for Lung Research (DZL) MarburgMarburgGermany
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Influenza and COVID-19 Co-infection. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2022. [DOI: 10.5812/archcid-131750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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