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Singh P, Sharma K, Bhargava A, Negi SS. Genomic characterization of Influenza A (H1N1)pdm09 and SARS-CoV-2 from Influenza Like Illness (ILI) and Severe Acute Respiratory Illness (SARI) cases reported between July-December, 2022. Sci Rep 2024; 14:10660. [PMID: 38724525 PMCID: PMC11081947 DOI: 10.1038/s41598-024-58993-w] [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: 01/13/2024] [Accepted: 04/05/2024] [Indexed: 05/12/2024] Open
Abstract
Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) cases are more prone to Influenza and SARS-CoV-2 infection. Accordingly, we genetically characterized Influenza and SARS-CoV-2 in 633 ILI and SARI cases by rRT-PCR and WGS. ILI and SARI cases showed H1N1pdm09 prevalence of 20.9% and 23.2% respectively. 135 (21.3%) H1N1pdm09 and 23 (3.6%) H3N2 and 5 coinfection (0.78%) of H1N1pdm09 and SARS-CoV-2 were detected. Phylogenetic analysis revealed H1N1pdm09 resemblance to clade 6B.1A.5a.2 and their genetic relatedness to InfA/Perth/34/2020, InfA/Victoria/88/2020 and InfA/Victoria/2570/2019. Pan 24 HA and 26 NA nonsynonymous mutations and novel HA (G6D, Y7F, Y78H, P212L, G339R, T508K and S523T) and NA (S229A) mutations were observed. S74R, N129D, N156K, S162N, K163Q and S164T alter HA Cb and Sa antibody recognizing site. Similarly, M19T, V13T substitution and multiple mutations in transmembrane and NA head domain drive antigenic drift. SARS-CoV-2 strains genetically characterized to Omicron BA.2.75 lineage containing thirty nonsynonymous spike mutations exhibited enhanced virulence and transmission rates. Coinfection although detected very minimal, the mutational changes in H1N1pdm09 and SARS-CoV-2 virus infected individuals could alter antibody receptor binding sites, allowing the viruses to escape immune response resulting in better adaptability and transmission. Thus continuous genomic surveillance is required to tackle any future outbreak.
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Affiliation(s)
- Pushpendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Kuldeep Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Anudita Bhargava
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India
| | - Sanjay Singh Negi
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India.
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Chheda P, Shivaprakash S, Bhalerao R, Biyani N. Epidemiological pattern of common respiratory viruses: A year-long study. Indian J Med Microbiol 2024; 49:100614. [PMID: 38759793 DOI: 10.1016/j.ijmmb.2024.100614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 04/12/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Affiliation(s)
- Pratiksha Chheda
- Department of Molecular Diagnostics, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai, India
| | - Shashikala Shivaprakash
- Department of Microbiology, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai, India.
| | - Rahul Bhalerao
- Department of Molecular Diagnostics, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai, India
| | - Neetu Biyani
- Department of Microbiology, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai, India
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Owusu D, Ndegwa LK, Ayugi J, Kinuthia P, Kalani R, Okeyo M, Otieno NA, Kikwai G, Juma B, Munyua P, Kuria F, Okunga E, Moen AC, Emukule GO. Use of Sentinel Surveillance Platforms for Monitoring SARS-CoV-2 Activity: Evidence From Analysis of Kenya Influenza Sentinel Surveillance Data. JMIR Public Health Surveill 2024; 10:e50799. [PMID: 38526537 PMCID: PMC11002741 DOI: 10.2196/50799] [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: 07/19/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Little is known about the cocirculation of influenza and SARS-CoV-2 viruses during the COVID-19 pandemic and the use of respiratory disease sentinel surveillance platforms for monitoring SARS-CoV-2 activity in sub-Saharan Africa. OBJECTIVE We aimed to describe influenza and SARS-CoV-2 cocirculation in Kenya and how the SARS-CoV-2 data from influenza sentinel surveillance correlated with that of universal national surveillance. METHODS From April 2020 to March 2022, we enrolled 7349 patients with severe acute respiratory illness or influenza-like illness at 8 sentinel influenza surveillance sites in Kenya and collected demographic, clinical, underlying medical condition, vaccination, and exposure information, as well as respiratory specimens, from them. Respiratory specimens were tested for influenza and SARS-CoV-2 by real-time reverse transcription polymerase chain reaction. The universal national-level SARS-CoV-2 data were also obtained from the Kenya Ministry of Health. The universal national-level SARS-CoV-2 data were collected from all health facilities nationally, border entry points, and contact tracing in Kenya. Epidemic curves and Pearson r were used to describe the correlation between SARS-CoV-2 positivity in data from the 8 influenza sentinel sites in Kenya and that of the universal national SARS-CoV-2 surveillance data. A logistic regression model was used to assess the association between influenza and SARS-CoV-2 coinfection with severe clinical illness. We defined severe clinical illness as any of oxygen saturation <90%, in-hospital death, admission to intensive care unit or high dependence unit, mechanical ventilation, or a report of any danger sign (ie, inability to drink or eat, severe vomiting, grunting, stridor, or unconsciousness in children younger than 5 years) among patients with severe acute respiratory illness. RESULTS Of the 7349 patients from the influenza sentinel surveillance sites, 76.3% (n=5606) were younger than 5 years. We detected any influenza (A or B) in 8.7% (629/7224), SARS-CoV-2 in 10.7% (768/7199), and coinfection in 0.9% (63/7165) of samples tested. Although the number of samples tested for SARS-CoV-2 from the sentinel surveillance was only 0.2% (60 per week vs 36,000 per week) of the number tested in the universal national surveillance, SARS-CoV-2 positivity in the sentinel surveillance data significantly correlated with that of the universal national surveillance (Pearson r=0.58; P<.001). The adjusted odds ratios (aOR) of clinical severe illness among participants with coinfection were similar to those of patients with influenza only (aOR 0.91, 95% CI 0.47-1.79) and SARS-CoV-2 only (aOR 0.92, 95% CI 0.47-1.82). CONCLUSIONS Influenza substantially cocirculated with SARS-CoV-2 in Kenya. We found a significant correlation of SARS-CoV-2 positivity in the data from 8 influenza sentinel surveillance sites with that of the universal national SARS-CoV-2 surveillance data. Our findings indicate that the influenza sentinel surveillance system can be used as a sustainable platform for monitoring respiratory pathogens of pandemic potential or public health importance.
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Affiliation(s)
- Daniel Owusu
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Linus K Ndegwa
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jorim Ayugi
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Rosalia Kalani
- Disease Surveillance and Response Unit, Ministry of Health, Nairobi, Kenya
| | - Mary Okeyo
- National Influenza Centre Laboratory, National Public Health Laboratories, Ministry of Health, Nairobi, Kenya
| | - Nancy A Otieno
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Gilbert Kikwai
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Bonventure Juma
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Peninah Munyua
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Francis Kuria
- Directorate of Public Health, Ministry of Health, Nairobi, Kenya
| | - Emmanuel Okunga
- Disease Surveillance and Response Unit, Ministry of Health, Nairobi, Kenya
| | - Ann C Moen
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gideon O Emukule
- Global Influenza Branch, Influenza Division, US Centers for Disease Control and Prevention, Nairobi, Kenya
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Sabastin M, Mone K, Manivel A, Cherayi Padinakarai A, Krishnasamy K. Epidemic profile of common respiratory viruses in association SARS CoV-2 among SARI and ARI-two year study. Mol Biol Rep 2024; 51:156. [PMID: 38252354 DOI: 10.1007/s11033-023-09084-y] [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: 09/07/2023] [Accepted: 11/30/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND COVID-19/SARS CoV-2 continue to pose a threat to human health and placed millions of livelihoods at risk. Surveillance for the other circulating seasonal viruses during this pandemic is necessary to understand the manifestations of the CoV-2 pandemic and their incidence. METHODS A detailed study survey was performed on subjects with acute respiratory infections (ARI) and severe acute respiratory infection (SARI) in the King Institute of Preventive Medicine and Research, Chennai from April 2020 to March 2022. A total of 1480 patients presenting with either SARI (41.8%) or ARI (58.1%) were screened for SARS CoV-2 and other respiratory viruses. The SARS CoV-2 real-time PCR was carried out using ICMR-approved kits and other respiratory viruses were detected using the commercially available real-time kit. RESULTS Out of the 620 SARI patients, 198 (31.9%) were positive for SARS CoV-2 RNA. Out of the 860 ARI patients, 352 (40.9%) were positive for SARS CoV-2 RNA. Among the 550 patients positive for SARS CoV-2, 7 (1.2%) were positive coexistent with other respiratory viruses. Among the 930 patients with negative SARS CoV-2, 222 (23.8%) were positive for other common respiratory viruses (p = 0.001). Influenza viruses (36.9%) predominated followed by RSV (31.9%) and Parainfluenza virus (13.5%). CONCLUSION This study suggests that viral coinfections are significantly higher among SARS CoV-2 negative individuals (23.8 vs. 1.2%). It is possibly due to viral interference and the competitive advantage of SARS CoV-2 in modulating the host immunity. Continuous surveillance is necessary for understanding the viral co-infection mechanisms.
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Affiliation(s)
- Merlin Sabastin
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - Kiruthiga Mone
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | - ArunKumar Manivel
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India
| | | | - Kaveri Krishnasamy
- Department of Virology, King Institute of Preventive Medicine and Research, Chennai, Tamil Nadu, India.
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Potdar V, Vijay N, Vipat V, Jadhav S, Gupta N, Aggarwal N. External quality assessment for laboratories in pan-India ILI/SARI surveillance for simultaneous detection of influenza virus and SARS-CoV-2. Front Public Health 2023; 11:1274508. [PMID: 38026348 PMCID: PMC10679675 DOI: 10.3389/fpubh.2023.1274508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The Indian Council of Medical Research has set up a nationwide network of 28 laboratories for simultaneous surveillance of influenza virus and SARS-CoV-2 in ILI/SARI patients, using an in-house developed and validated multiplex real-time RTPCR assay. The aim of this study was to ensure the quality of testing by these laboratories by implementing an external quality assessment program (EQAP). Methods For this EQAP, a proficiency test (PT) panel comprising tissue-culture or egg-grown influenza virus and SARS-CoV-2 was developed. The PT panel was distributed to all the participant laboratories, which tested the panel and submitted the qualitative results online to the EQAP provider. The performance of the laboratories was evaluated on qualitative criteria but cycle threshold (Ct) values were also gathered for each sample. Results On a qualitative basis, all the laboratories achieved the criteria of 90% concordance with the results of the PT panel provider. Ct values of different samples across the laboratories were within ≤ ±3 cycles of the corresponding mean values of the respective sample. The results of this EQAP affirmed the quality and reliability of testing being done for simultaneous surveillance of influenza virus and SARS-CoV-2 in India.
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Affiliation(s)
- Varsha Potdar
- Indian Council of Medical Research–National Institute of Virology, Pune, India
| | - Neetu Vijay
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Veena Vipat
- Indian Council of Medical Research–National Institute of Virology, Pune, India
| | - Sheetal Jadhav
- Indian Council of Medical Research–National Institute of Virology, Pune, India
| | - Nivedita Gupta
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Neeraj Aggarwal
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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Varshney K, Pillay P, Mustafa AD, Shen D, Adalbert JR, Mahmood MQ. A systematic review of the clinical characteristics of influenza-COVID-19 co-infection. Clin Exp Med 2023; 23:3265-3275. [PMID: 37326928 PMCID: PMC10618381 DOI: 10.1007/s10238-023-01116-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
COVID-19 has impacted populations across the globe and has been a major cause of morbidity and mortality. Influenza is another potentially deadly respiratory infection that affects people worldwide. While both of these infections pose major health threats, little is currently understood regarding the clinical aspects of influenza and COVID-19 co-infection. Our objective was to therefore provide a systematic review of the clinical characteristics, treatments, and outcomes for patients who are co-infected with influenza and COVID-19. Our review, which was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, involved searching for literature in seven different databases. Studies were eligible for inclusion if they included at least one co-infected patient, were available in English, and described clinical characteristics for the patients. Data were pooled after extraction. Study quality was assessed using the Joanna Brigg's Institute Checklists. Searches produced a total of 5096 studies, and of those, 64 were eligible for inclusion. A total of 6086 co-infected patients were included, 54.1% of whom were male; the mean age of patients was 55.9 years (SD = 12.3). 73.6% of cases were of influenza A and 25.1% were influenza B. 15.7% of co-infected patients had a poor outcome (death/deterioration). The most common symptoms were fever, cough, and dyspnea, with the most frequent complications being pneumonia, linear atelectasis, and acute respiratory distress syndrome. Oseltamivir, supplemental oxygen, arbidol, and vasopressors were the most common treatments provided to patients. Having comorbidities, and being unvaccinated for influenza, were shown to be important risk factors. Co-infected patients show symptoms that are similar to those who are infected with COVID-19 or influenza only. However, co-infected patients have been shown to be at an elevated risk for poor outcomes compared to mono-infected COVID-19 patients. Screening for influenza in high-risk COVID-19 patients is recommended. There is also a clear need to improve patient outcomes with more effective treatment regimens, better testing, and higher rates of vaccination.
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Affiliation(s)
- Karan Varshney
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, VIC, 3216, Australia.
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia.
| | - Preshon Pillay
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, VIC, 3216, Australia
| | - Ashmit Daiyan Mustafa
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, VIC, 3216, Australia
| | - Dennis Shen
- School of Medicine, University of New England, Armidale, NSW, Australia
| | | | - Malik Quasir Mahmood
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, VIC, 3216, Australia
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Potdar V, Vijay N, Mukhopadhyay L, Aggarwal N, Bhardwaj SD, Choudhary ML, Gupta N, Kaur H, Narayan J, Kumar P, Singh H, Abdulkader RS, Murhekar M, Mishra M, Thangavel S, Nagamani K, Dhodapkar R, Fomda BA, Varshney U, Majumdar A, Dutta S, Vijayachari P, Turuk J, Majumdar T, Sahoo GC, Pandey K, Bhargava A, Negi SS, Khatri PK, Kalawat U, Biswas D, Khandelwal N, Borkakoty B, Manjushree S, Singh MP, Iravane J, Kaveri K, Shantala GB, Brijwal M, Choudhary A, Dar L, Malhotra B, Jain A. Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis. Front Public Health 2023; 11:1218292. [PMID: 37927860 PMCID: PMC10624221 DOI: 10.3389/fpubh.2023.1218292] [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: 05/06/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023] Open
Abstract
Background Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2. Methods In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022. Findings Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8 years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement. Interpretation The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.
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Affiliation(s)
| | - Neetu Vijay
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Labanya Mukhopadhyay
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Neeraj Aggarwal
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | | | | | - Nivedita Gupta
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Harmanmeet Kaur
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Jitendra Narayan
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Prabhat Kumar
- Biomedical Informatics (BMI) Division, Indian Council of Medical Research, New Delhi, India
| | - Harpreet Singh
- Biomedical Informatics (BMI) Division, Indian Council of Medical Research, New Delhi, India
| | | | | | - Meena Mishra
- VRDL, All India Institute of Medical Sciences, Nagpur, India
| | | | - K. Nagamani
- VRDL, Gandhi Medical College, Secunderabad, India
| | - Rahul Dhodapkar
- VRDL, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | | | | | - Agniva Majumdar
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - P. Vijayachari
- ICMR-Regional Medical Research Centre, Port Blair, India
| | | | | | | | - Krishna Pandey
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | | | | | | | - Usha Kalawat
- VRDL, Sri Venkateswara Institute of Medical Sciences, Tirupati, India
| | - Debasis Biswas
- VRDL, All India Institute of Medical Sciences, Bhopal, India
| | | | | | | | - Mini P. Singh
- VRDL, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | - K. Kaveri
- VRDL, King Institute of Preventive Medicine and Research, Chennai, India
| | - G. B. Shantala
- VRDL, Bangalore Medical College and Research Institute, Bangalore, India
| | - Megha Brijwal
- VRDL, All India Institute of Medical Sciences, New Delhi, India
| | | | - Lalit Dar
- VRDL, All India Institute of Medical Sciences, New Delhi, India
| | | | - Amita Jain
- VRDL, King George’s Medical University, Lucknow, India
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Krishnan A. Need for a robust public health response to seasonal influenza in India. Indian J Med Res 2023; 157:421-426. [PMID: 37955218 PMCID: PMC10443721 DOI: 10.4103/ijmr.ijmr_184_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Indexed: 11/14/2023] Open
Affiliation(s)
- Anand Krishnan
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi 110 029, India
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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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Korsun N, Trifonova I, Dobrinov V, Madzharova I, Grigorova I, Christova I. Low prevalence of influenza viruses and predominance of A(H3N2) virus with respect to SARS-CoV-2 during the 2021-2022 season in Bulgaria. J Med Virol 2023; 95:e28489. [PMID: 36832544 PMCID: PMC10107854 DOI: 10.1002/jmv.28489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
Social distancing, mask-wearing, and travel restrictions during the COVID-19 pandemic have significantly impacted the spread of influenza viruses. The objectives of this study were to analyze the pattern of influenza virus circulation with respect to that of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Bulgaria during the 2021-2022 season and to perform a phylogenetic/molecular analysis of the hemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains. Influenza infection was confirmed using real-time reverse transcription polymerase chain reaction in 93 (4.2%) of the 2193 patients with acute respiratory illness tested wherein all detected viruses were subtyped as A(H3N2). SARS-CoV-2 was identified in 377 (24.3%) of the 1552 patients tested. Significant differences in the incidence of influenza viruses and SARS-CoV-2 were found between individual age groups, outpatients/inpatients, and in the seasonal distribution of cases. Two cases of coinfections were identified. In hospitalized patients, the Ct values of influenza viruses at admission were lower in adults aged ≥65 years (indicating higher viral load) than in children aged 0-14 years (p < 0.05). In SARS-CoV-2-positive inpatients, this association was not statistically significant. HA genes of all A(H3N2) viruses analyzed belonged to subclade 3C.2a1b.2a. The sequenced viruses carried 11 substitutions in HA and 5 in NA, in comparison to the vaccine virus A/Cambodia/e0826360/2020, including several substitutions in the HA antigenic sites B and C. This study revealed extensive changes in the typical epidemiology of influenza infection, including a dramatic reduction in the number of cases, diminished genetic diversity of circulating viruses, changes in age, and seasonal distribution of cases.
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Affiliation(s)
- Neli Korsun
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Ivelina Trifonova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Veselin Dobrinov
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iveta Madzharova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iliyana Grigorova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iva Christova
- National Laboratory "Influenza and ARI", Department of Virology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
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Alhumaid S, Alabdulqader M, Al Dossary N, Al Alawi Z, Alnaim AA, Al Mutared KM, Al Noaim K, Al Ghamdi MA, Albahrani SJ, Alahmari AA, Al Hajji Mohammed SM, Almatawah YA, Bayameen OM, Alismaeel AA, Alzamil SK, Alturki SA, Albrahim ZR, Al Bagshi NA, Alshawareb HY, Alhudar JA, Algurairy QA, Alghadeer SM, Alhadab HA, Aljubran TN, Alabdulaly YA, Al Mutair A, Rabaan AA. Global Coinfections with Bacteria, Fungi, and Respiratory Viruses in Children with SARS-CoV-2: A Systematic Review and Meta-Analysis. Trop Med Infect Dis 2022; 7:tropicalmed7110380. [PMID: 36422931 PMCID: PMC9698370 DOI: 10.3390/tropicalmed7110380] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Coinfection with bacteria, fungi, and respiratory viruses has been described as a factor associated with more severe clinical outcomes in children with COVID-19. Such coinfections in children with COVID-19 have been reported to increase morbidity and mortality. Objectives: To identify the type and proportion of coinfections with SARS-CoV-2 and bacteria, fungi, and/or respiratory viruses, and investigate the severity of COVID-19 in children. Methods: For this systematic review and meta-analysis, we searched ProQuest, Medline, Embase, PubMed, CINAHL, Wiley online library, Scopus, and Nature through the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for studies on the incidence of COVID-19 in children with bacterial, fungal, and/or respiratory coinfections, published from 1 December 2019 to 1 October 2022, with English language restriction. Results: Of the 169 papers that were identified, 130 articles were included in the systematic review (57 cohort, 52 case report, and 21 case series studies) and 34 articles (23 cohort, eight case series, and three case report studies) were included in the meta-analysis. Of the 17,588 COVID-19 children who were tested for co-pathogens, bacterial, fungal, and/or respiratory viral coinfections were reported (n = 1633, 9.3%). The median patient age ranged from 1.4 months to 144 months across studies. There was an increased male predominance in pediatric COVID-19 patients diagnosed with bacterial, fungal, and/or viral coinfections in most of the studies (male gender: n = 204, 59.1% compared to female gender: n = 141, 40.9%). The majority of the cases belonged to White (Caucasian) (n = 441, 53.3%), Asian (n = 205, 24.8%), Indian (n = 71, 8.6%), and Black (n = 51, 6.2%) ethnicities. The overall pooled proportions of children with laboratory-confirmed COVID-19 who had bacterial, fungal, and respiratory viral coinfections were 4.73% (95% CI 3.86 to 5.60, n = 445, 34 studies, I2 85%, p < 0.01), 0.98% (95% CI 0.13 to 1.83, n = 17, six studies, I2 49%, p < 0.08), and 5.41% (95% CI 4.48 to 6.34, n = 441, 32 studies, I2 87%, p < 0.01), respectively. Children with COVID-19 in the ICU had higher coinfections compared to ICU and non-ICU patients, as follows: respiratory viral (6.61%, 95% CI 5.06−8.17, I2 = 0% versus 5.31%, 95% CI 4.31−6.30, I2 = 88%) and fungal (1.72%, 95% CI 0.45−2.99, I2 = 0% versus 0.62%, 95% CI 0.00−1.55, I2 = 54%); however, COVID-19 children admitted to the ICU had a lower bacterial coinfection compared to the COVID-19 children in the ICU and non-ICU group (3.02%, 95% CI 1.70−4.34, I2 = 0% versus 4.91%, 95% CI 3.97−5.84, I2 = 87%). The most common identified virus and bacterium in children with COVID-19 were RSV (n = 342, 31.4%) and Mycoplasma pneumonia (n = 120, 23.1%). Conclusion: Children with COVID-19 seem to have distinctly lower rates of bacterial, fungal, and/or respiratory viral coinfections than adults. RSV and Mycoplasma pneumonia were the most common identified virus and bacterium in children infected with SARS-CoV-2. Knowledge of bacterial, fungal, and/or respiratory viral confections has potential diagnostic and treatment implications in COVID-19 children.
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Affiliation(s)
- Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
- Correspondence: ; Tel.: +966-561-522-581
| | - Muneera Alabdulqader
- Pediatric Nephrology Specialty, Pediatric Department, Medical College, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Nourah Al Dossary
- General Surgery Department, Alomran General Hospital, Ministry of Health, Al-Ahsa 36358, Saudi Arabia
| | - Zainab Al Alawi
- Division of Allergy and Immunology, College of Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Abdulrahman A. Alnaim
- Department of Pediatrics, College of Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Koblan M. Al Mutared
- Administration of Pharmaceutical Care, Ministry of Health, Najran 66255, Saudi Arabia
| | - Khalid Al Noaim
- Department of Pediatrics, College of Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Mohammed A. Al Ghamdi
- Department of Pediatrics, King Fahad Hospital of the University, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Suha Jafar Albahrani
- Division of Diabetology, Family Medicine Department, College of Medicine, King Faisal University, Al-Ahsa 36364, Saudi Arabia
| | - Abdulaziz A. Alahmari
- Department of Pediatrics, King Fahad Hospital of the University, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | | | - Yameen Ali Almatawah
- Division of Infectious Diseases and Infection Control, Pediatric Department, Maternity and Children Hospital, Ministry of Health, Al-Ahsa 36422, Saudi Arabia
| | - Omar Musa Bayameen
- Public Health Administration, Directorate of Health Affairs, Ministry of Health, Al-Ahsa 36441, Saudi Arabia
| | - Ahmed Abdulwhab Alismaeel
- Public Health Administration, Directorate of Health Affairs, Ministry of Health, Al-Ahsa 36441, Saudi Arabia
| | - Sherifah Khaled Alzamil
- Public Health Administration, Directorate of Health Affairs, Ministry of Health, Al-Ahsa 36441, Saudi Arabia
| | - Samiah Ahmad Alturki
- Public Health Administration, Directorate of Health Affairs, Ministry of Health, Al-Ahsa 36441, Saudi Arabia
| | - Zahra’a Radi Albrahim
- Public Health Administration, Directorate of Health Affairs, Ministry of Health, Al-Ahsa 36441, Saudi Arabia
| | - Nasreen Ahmad Al Bagshi
- Public Health Administration, Directorate of Health Affairs, Ministry of Health, Al-Ahsa 36441, Saudi Arabia
| | - Hesham Yousef Alshawareb
- Southern Sector, Primary Care Medicine, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 36421, Saudi Arabia
| | - Jaafar Abdullah Alhudar
- Regional Medical Supply, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 36361, Saudi Arabia
| | | | - Samirah Mansour Alghadeer
- Infection Prevention and Control Administration, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 36421, Saudi Arabia
| | - Hassan Ali Alhadab
- Ambulatory Transportation Administration, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 36421, Saudi Arabia
| | | | - Yousif Ahmad Alabdulaly
- Quality Assurance and Patient Safety Administration, Directorate of Health Affairs, Ministry of Health, Al-Ahsa 36441, Saudi Arabia
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia
- College of Nursing, Princess Norah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia
- Department of Nursing, Prince Sultan Military College, Dhahran 34313, Saudi Arabia
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health/Nutrition, The University of Haripur, Haripur 22620, Khyber Pakhtunkhwa, Pakistan
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Ceccarelli G, d'Ettorre G, Russo A, Fabris S, Ciccozzi M, d'Ettorre G. SARS-CoV-2 pandemic, influenza, and influenza-like illness epidemics: Allies or enemies? J Med Virol 2022; 95:e28148. [PMID: 36114792 PMCID: PMC9538197 DOI: 10.1002/jmv.28148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/23/2022] [Accepted: 09/12/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Giancarlo Ceccarelli
- Department of Public Health and Infectious DiseasesUniversity of Rome SapienzaRomeItaly
- Scientific CommitteeMigrant and Global Health Research Organization (Mi‐Hero)RomeItaly
| | | | - Alessandro Russo
- Department of Medical and Surgical Sciences, “Magna Græcia”University of CatanzaroCatanzaroItaly
| | - Silvia Fabris
- Medical Statistics and Molecular Epidemiology UnitUniversity Campus Bio‐Medico of RomeRomeItaly
| | - Massimo Ciccozzi
- Medical Statistics and Molecular Epidemiology UnitUniversity Campus Bio‐Medico of RomeRomeItaly
| | - Gabriella d'Ettorre
- Department of Public Health and Infectious DiseasesUniversity of Rome SapienzaRomeItaly
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Trifonova I, Christova I, Madzharova I, Angelova S, Voleva S, Yordanova R, Tcherveniakova T, Krumova S, Korsun N. Clinical significance and role of coinfections with respiratory pathogens among individuals with confirmed severe acute respiratory syndrome coronavirus-2 infection. Front Public Health 2022; 10:959319. [PMID: 36117597 PMCID: PMC9479447 DOI: 10.3389/fpubh.2022.959319] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/04/2022] [Indexed: 01/24/2023] Open
Abstract
Introduction This study aimed to determine the prevalence, viral profile, and clinical features of coinfections with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and other respiratory viruses. Methods Nasopharyngeal samples and clinical data of 221 hospitalized patients and 21 outpatients were collected and analyzed. Real-time reverse transcription-polymerase chain reaction was used to detect SARS-CoV-2, influenza virus, respiratory syncytial virus (RSV), human metapneumovirus (HMPV), parainfluenza virus (PIV) 1,2,3, rhinovirus (RV), adenovirus (AdV), bocaviruses (BoV), and seasonal coronaviruses (OC43, 229E, NL63, and HKU1). Viral load was determined by capillary electrophoresis. Results From November 2020 to mid-March 2022, 242 SARS-CoV-2 positive patients were tested for seasonal respiratory viruses, and 24 (9.9%) cases of coinfections were detected. The distribution of viruses involved in cases of coinfections were as follows: HMPV (n = 6; 25%), RSV (n = 4;16.7%), AdV (n = 4; 16.7%), BoV (n = 4; 16.7%), PIV3 (n = 2; 8.3%), influenza A (H3N2; n = 2; 8.3%), RV (n = 1; 4.62%), and RV+BoV (n = 1; 4.62%). The proportion of detected coinfections with SARS-CoV-2 was highest in children aged 0-5 years (59%), followed by those >65 years (33%). In specimens with detected coinfection, the viral load of influenza was higher than that of SARS-CoV-2, and the mean viral load of SARS-CoV-2 was higher than that of the other respiratory viruses. C-reactive protein (CRP) and lymphocytes count in co-infected patients >65 years of age were on average higher than in children <16 years of age (mean CRP of 161.8 ± 133.1 mg/L; 19.7 ± 3.09% vs. mean 6.9 ± 8.9 mg/L, 0.9 ± 3.1%; p < 0.01). Patients >65 years of age co-infected with SARS-CoV-2 and other respiratory viruses had longer hospital stays than those <16 years of age (mean 9 ± 3.96 days vs. 5.44 ± 1.89 days; p = 0.025). The combination of AdV and SARS-CoV-2 is fatal for patients aged >65 years. Conclusion In patients aged >65 years, coinfection with SARS CoV-2 and other respiratory viruses, together with concomitant diseases, causes worsening of the clinical picture and complications, and can be fatal. Screening of patients with SARS CoV-2 for other respiratory viruses is needed to select appropriate treatments and prevent a fatal outcome of the disease.
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Affiliation(s)
- Ivelina Trifonova
- National Laboratory “Influenza and ARD”, Department of Virology, National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iva Christova
- National Laboratory “Influenza and ARD”, Department of Virology, National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iveta Madzharova
- National Laboratory “Influenza and ARD”, Department of Virology, National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Svetla Angelova
- Clinical Virology Laboratory, University Hospital “Prof. Dr. Stoyan Kirkovich”, Stara Zagora, Bulgaria
| | - Silvya Voleva
- Clinic for Neuro Infections, Airborne, Roof, and Transmissible Infections, Infectious Hospital “Prof. Ivan Kirov”, Department of Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Ralitsa Yordanova
- Clinic for Neuro Infections, Airborne, Roof, and Transmissible Infections, Infectious Hospital “Prof. Ivan Kirov”, Department of Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Tatiana Tcherveniakova
- Clinic for Neuro Infections, Airborne, Roof, and Transmissible Infections, Infectious Hospital “Prof. Ivan Kirov”, Department of Infectious Diseases, Parasitology and Tropical Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Stefka Krumova
- National Laboratory “Influenza and ARD”, Department of Virology, National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Neli Korsun
- National Laboratory “Influenza and ARD”, Department of Virology, National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
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