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Soetikno AG, Lundberg AL, Ozer EA, Wu SA, Welch SB, Mason M, Liu Y, Havey RJ, Murphy RL, Hawkins C, Moss CB, Post LA. Updated Surveillance Metrics and History of the COVID-19 Pandemic (2020-2023) in the Middle East and North Africa: Longitudinal Trend Analysis. JMIR Public Health Surveill 2024; 10:e53219. [PMID: 38568184 PMCID: PMC11208839 DOI: 10.2196/53219] [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: 10/03/2023] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND This study updates the COVID-19 pandemic surveillance in the Middle East and North Africa (MENA) we first conducted in 2020 with 2 additional years of data for the region. OBJECTIVE The objective of this study is to determine whether the MENA region meets the criteria for moving from a pandemic to endemic. In doing so, this study considers pandemic trends, dynamic and genomic surveillance methods, and region-specific historical context for the pandemic. These considerations continue through the World Health Organization (WHO) declaration of the end of the public health emergency for the COVID-19 pandemic on May 5, 2023. METHODS In addition to updates to traditional surveillance data and dynamic panel estimates from the original study by Post et al, this study used data on sequenced SARS-CoV-2 variants from the Global Initiative on Sharing All Influenza Data (GISAID) to identify the appearance and duration of variants of concern. We used Nextclade nomenclature to collect clade designations from sequences and Pangolin nomenclature for lineage designations of SARS-CoV-2. Finally, we conducted a 1-sided t test to determine whether regional weekly speed of COVID-19 spread was greater than an outbreak threshold of 10. We ran the test iteratively with 6 months of data from September 4, 2020, to May 12, 2023. RESULTS The speed of COVID-19 spread for the region had remained below the outbreak threshold for 7 continuous months by the time of the WHO declaration. Acceleration and jerk were also low and stable. Although the 1- and 7-day persistence coefficients remained statistically significant and positive, the weekly shift parameters suggested the coefficients had most recently turned negative, meaning the clustering effect of new COVID-19 cases became even smaller in the 2 weeks around the WHO declaration. From December 2021 onward, Omicron was the predominant variant of concern in sequenced viral samples. The rolling t test of the speed of spread equal to 10 became entirely insignificant from October 2022 onward. CONCLUSIONS The COVID-19 pandemic had far-reaching effects on MENA, impacting health care systems, economies, and social well-being. Although COVID-19 continues to circulate in the MENA region, the rate of transmission remained well below the threshold of an outbreak for over 1 year ahead of the WHO declaration. COVID-19 is endemic in the region and no longer reaches the threshold of the pandemic definition. Both standard and enhanced surveillance metrics confirm that the pandemic had transitioned to endemic by the time of the WHO declaration.
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Affiliation(s)
- Alan G Soetikno
- Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Alexander L Lundberg
- Buehler Center for Health Policy and Economics, Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Scott A Wu
- Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Sarah B Welch
- Buehler Center for Health Policy and Economics, Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Maryann Mason
- Buehler Center for Health Policy and Economics, Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Yingxuan Liu
- Buehler Center for Health Policy and Economics, Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Robert J Havey
- Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Medicine, General Internal Medicine and Geriatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Robert L Murphy
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Claudia Hawkins
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Center for Global Communicable and Emerging Infectious Diseases, Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Charles B Moss
- Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Lori Ann Post
- Buehler Center for Health Policy and Economics, Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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Boussarsar M, Ennouri E, Habbachi N, Bouguezzi N, Meddeb K, Gallas S, Hafdhi M, Zghidi M, Toumi R, Ben Saida I, Abid S, Boutiba-Ben Boubaker I, Maazaoui L, El Ghord H, Gzara A, Yazidi R, Ben Salah A. Epidemiology and burden of Severe Acute Respiratory Infections (SARI) in the aftermath of COVID-19 pandemic: A prospective sentinel surveillance study in a Tunisian Medical ICU, 2022/2023. PLoS One 2023; 18:e0294960. [PMID: 38100529 PMCID: PMC10723666 DOI: 10.1371/journal.pone.0294960] [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: 08/04/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Severe Acute Respiratory Infections (SARI) caused by influenza and other respiratory viruses pose significant global health challenges, and the COVID-19 pandemic has further strained healthcare systems. As the focus shifts from the pandemic to other respiratory infections, assessing the epidemiology and burden of SARI is crucial for healthcare planning and resource allocation. Aim: to understand the impact of the post-pandemic period on the epidemiology of SARI cases, clinical outcomes, and healthcare resource utilization in Tunisia. METHODS This is a prospective study conducted in a Tunisian MICU part of a national sentinel surveillance system, focusing on enhanced SARI surveillance. SARI cases from week 39/2022, 26 September to week 19/2023, 13 May were included, according to a standardized case definition. Samples were collected for virological RT-PCR testing, and an electronic system ensured standardized and accurate data collection. Descriptive statistics were performed to assess epidemiology, trends, and outcomes of SARI cases, and univariate/multivariate analyses to assess factors associated with mortality. RESULTS Among 312 MICU patients, 164 SARI cases were identified during the study period. 64(39%) RT-PCR were returned positive for at least one pathogen, with influenza A and B strains accounting for 20.7% of cases at the early stages of the influenza season. The MICU experienced a significant peak in admissions during weeks 1-11/2023, leading to resource mobilization and the creation of a surge unit. SARI cases utilized 1664/3120 of the MICU-stay days and required 1157 mechanical ventilation days. The overall mortality rate among SARI cases was 22.6%. Age, non-COPD, and ARDS were identified as independent predictors of mortality. CONCLUSIONS The present study identified a relatively high rate of SARI cases, with 39% positivity for at least one respiratory virus, with influenza A and B strains occurring predominantly during the early stages of the influenza season. The findings shed light on the considerable resource utilization and mortality associated with these infections, underscoring the urgency for proactive management and efficient resource allocation strategies.
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Affiliation(s)
- Mohamed Boussarsar
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
- Medical Intensive Care Unit, Research Laboratory “Heart Failure”, Farhat Hached University Hospital, Sousse, Tunisia
| | - Emna Ennouri
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
- Medical Intensive Care Unit, Research Laboratory “Heart Failure”, Farhat Hached University Hospital, Sousse, Tunisia
| | - Naima Habbachi
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
| | - Nabil Bouguezzi
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
- Medical Intensive Care Unit, Research Laboratory “Heart Failure”, Farhat Hached University Hospital, Sousse, Tunisia
| | - Khaoula Meddeb
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
- Medical Intensive Care Unit, Research Laboratory “Heart Failure”, Farhat Hached University Hospital, Sousse, Tunisia
| | - Salma Gallas
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
- Medical Intensive Care Unit, Research Laboratory “Heart Failure”, Farhat Hached University Hospital, Sousse, Tunisia
| | - Malek Hafdhi
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
| | - Marwa Zghidi
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
- Medical Intensive Care Unit, Research Laboratory “Heart Failure”, Farhat Hached University Hospital, Sousse, Tunisia
| | - Radhouane Toumi
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
- Medical Intensive Care Unit, Research Laboratory “Heart Failure”, Farhat Hached University Hospital, Sousse, Tunisia
| | - Imen Ben Saida
- University of Sousse, Faculty of Medicine of Sousse, Sousse, Tunisia
- Medical Intensive Care Unit, Research Laboratory “Heart Failure”, Farhat Hached University Hospital, Sousse, Tunisia
| | - Salma Abid
- National Influenza Centre-Tunis, Unit Virology, Microbiology Laboratory, Charles Nicolle Hospital, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- National Influenza Centre-Tunis, Unit Virology, Microbiology Laboratory, Charles Nicolle Hospital, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis, Tunisia
| | | | | | - Ahlem Gzara
- Primary Health Care Directorate, Tunis, Tunisia
| | - Rihab Yazidi
- Laboratory of Transmission, Control and Immunobiology of Infections (LR11IPT02), Institut Pasteur de Tunis, Tunis-Belvédère, Tunisia
- Service of Medical Epidemiology, Institut Pasteur de Tunis, Tunis-Belvédère, Tunisia
- Laboratory of Transmission, Control and Immunobiology of Infections LR16IPT02, Institut Pasteur de Tunis, University of Tunis, El Manar, Tunis, Tunisia
| | - Afif Ben Salah
- Service of Medical Epidemiology, Institut Pasteur de Tunis, Tunis-Belvédère, Tunisia
- Department of Family and Community Medicine, College of Medicine and Medical Sciences (CMMS), Arabian Gulf University (AGU), Manama, Bahrain
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Sominina A, Danilenko D, Komissarov AB, Pisareva M, Fadeev A, Konovalova N, Eropkin M, Petrova P, Zheltukhina A, Musaeva T, Eder V, Ivanova A, Komissarova K, Stolyarov K, Karpova L, Smorodintseva E, Dorosh A, Krivitskaya V, Kuznetzova E, Majorova V, Petrova E, Boyarintseva A, Ksenafontov A, Shtro A, Nikolaeva J, Bakaev M, Burtseva E, Lioznov D. Assessing the Intense Influenza A(H1N1)pdm09 Epidemic and Vaccine Effectiveness in the Post-COVID Season in the Russian Federation. Viruses 2023; 15:1780. [PMID: 37632122 PMCID: PMC10458445 DOI: 10.3390/v15081780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 pandemic had a profound impact on influenza activity worldwide. However, as the pandemic progressed, influenza activity resumed. Here, we describe the influenza epidemic of high intensity of the 2022-2023 season. The epidemic had an early start and peaked in week 51.2022. The extremely high intensity of the epidemic may have been due to a significant decrease in herd immunity. The results of PCR-testing of 220,067 clinical samples revealed that the influenza A(H1N1)pdm09 virus dominated, causing 56.4% of positive cases, while A(H3N2) influenza subtype accounted for only 0.6%, and influenza B of Victoria lineage-for 34.3%. The influenza vaccine was found to be highly effective, with an estimated effectiveness of 92.7% in preventing admission with laboratory-confirmed influenza severe acute respiratory illness (SARI) cases and 54.7% in preventing influenza-like illness/acute respiratory illness (ILI/ARI) cases due to antigenic matching of circulated viruses with influenza vaccine strains for the season. Full genome next-generation sequencing of 1723 influenza A(H1N1)pdm09 viruses showed that all of them fell within clade 6B.1A.5.a2; nine of them possessed H275Y substitution in the NA gene, a genetic marker of oseltamivir resistance. Influenza A(H3N2) viruses belonged to subclade 3C.2a1b.2a.2 with the genetic group 2b being dominant. All 433 influenza B viruses belonged to subclade V1A.3a.2 encoding HA1 substitutions A127T, P144L, and K203R, which could be further divided into two subgroups. None of the influenza A(H3N2) and B viruses sequenced had markers of resistance to NA inhibitors. Thus, despite the continuing circulation of Omicron descendant lineages, influenza activity has resumed in full force, raising concerns about the intensity of fore coming seasonal epidemics.
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Affiliation(s)
- Anna Sominina
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Daria Danilenko
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Andrey B. Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Maria Pisareva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Artem Fadeev
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Nadezhda Konovalova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Mikhail Eropkin
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Polina Petrova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Alyona Zheltukhina
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Tamila Musaeva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Veronika Eder
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Anna Ivanova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Kseniya Komissarova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Kirill Stolyarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Ludmila Karpova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Elizaveta Smorodintseva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Anna Dorosh
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Vera Krivitskaya
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Elena Kuznetzova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Victoria Majorova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Ekaterina Petrova
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Anastassia Boyarintseva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Andrey Ksenafontov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Anna Shtro
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Julia Nikolaeva
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Mikhail Bakaev
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
| | - Elena Burtseva
- National Research Center for Epidemiology and Microbiology Named after N.F. Gamaleya, 123098 Moscow, Russia
| | - Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia; (D.D.); (E.K.)
- Department of Infectious Diseases, First Pavlov State Medical University, 197022 Saint Petersburg, Russia
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