Adapting an integrated acute respiratory infections sentinel surveillance to the COVID-19 pandemic requirements, Egypt, 2020–2022

Fahim, Manal; Elsood, Hanaa Abu; AbdElGawad, Basma; Deghedy, Ola; Naguib, Amel; Roshdy, Wael H.; Showky, Shymaa; Kamel, Reham; Elguindy, Nancy; AbdelFatah, Mohamad; Afifi, Salma; Kandeel, Amr; Abdelghaffar, Khaled

doi:10.1016/j.puhip.2023.100358

Cited by 5 publications

(10 citation statements)

References 23 publications

(26 reference statements)

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“…MoHP is monitoring influenza and SARS-CoV-2 activities through ARI integrated surveillance, National infectious Diseases surveillance (NEDSS), ARI syndromic surveillance, ARI mortality surveillance, and event-based surveillance (EBS) systems [ 12 ]. Furthermore, in 2016, RSV was introduced to the sentinel surveillance to monitor RSV among hospitalized children under the age of 2 years [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Resurgence of influenza and respiratory syncytial virus in Egypt following two years of decline during the COVID-19 pandemic: outpatient clinic survey of infants and children, October 2022

et al. 2023

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Introduction Two years after unprecedented low rates of circulation of most common respiratory viruses (SARS-CoV-2), the Egyptian ARI surveillance system detected an increase in acute respiratory infections (ARIs) with a reduced circulation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially among school children. A national survey was conducted to estimate the burden and identify the viral causes of ARIs among children < 16 years of age. Methods A one-day survey was carried out in 98 governmental outpatient clinics distributed all over Egypt 26 governorates. The four largest referral hospitals in each governorate where most influenza-like illness (ILI) patients seek care were selected. Using the WHO case definition, the first five patients < 16 years of age with ILI symptoms visiting the selected outpatient clinics on the survey day were enrolled. Basic demographic and clinical data of patients were collected using a linelist. Patients were swabbed and tested for SARS-CoV-2, influenza, and Respiratory Syncytial virus (RSV) by RT-PCR at the Central Laboratory in Cairo. Results Overall, 530 patients enrolled, their mean age was 5.8 ± 4.2, 57.1% were males, and 70.2% reside in rural or semi-rural areas. Of all patients, 134 (25.3%) had influenza, 111 (20.9%) RSV, and 14 (2.8%) coinfections. Influenza-positive children were older compared to RSV, (7.2 ± 4.1, 4.3 ± 4.1, p < 0.001), with more than half of them (53.0%) being school students. Dyspnea was reported in RSV more than in influenza (62.2% vs. 49.3%, p < 0.05). Among RSV patients, children < 2 years had a higher rate of dyspnea than others (86.7% vs. 53.1%, < 0.001). Conclusions A resurgence of influenza and RSV was detected in Egypt in the 2022–2023 winter season. Influenza caused a higher rate of infection than RSV, while RSV caused more severe symptoms than influenza. Monitoring a broader range of respiratory pathogens is recommended to estimate the ARI burden and risky groups for severe disease in Egypt.

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Section: Introductionmentioning

confidence: 99%

Resurgence of influenza and respiratory syncytial virus in Egypt following two years of decline during the COVID-19 pandemic: outpatient clinic survey of infants and children, October 2022

et al. 2023

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“…During the SARS‐CoV‐2 pandemic, many countries integrated SARS‐CoV‐2 surveillance in their existing sentinel surveillance systems successfully and allowed those countries to evaluate different epidemiological aspects of this new respiratory pathogen 9,30,37,46,47 . The Belgian National Influenza Centre also integrated SARS‐CoV‐2 detection in the existing hospital SARI surveillance for influenza 29 .…”

Section: Discussionmentioning

confidence: 99%

“…During the SARS-CoV-2 pandemic, many countries integrated SARS-CoV-2 surveillance in their existing sentinel surveillance systems successfully and allowed those countries to evaluate different epidemiological aspects of this new respiratory pathogen. 9,30,37,46,47 The Belgian National Influenza Centre also integrated SARS-CoV-2 detection in the existing hospital SARI surveillance for influenza. 29 This allowed sequencing of SARS-CoV-2 positive samples and thus variant genomic surveillance during the pandemic, resulting in a total of 964 sequences over the period 2020-W09 until 2022-W52.…”

Section: Discussionmentioning

confidence: 99%

“…In particular, SARI surveillance has proven to be very useful to evaluate the severity of infections caused by different respiratory viruses, including influenza virus. [27][28][29][30][33][34][35][36][37] Our group also demonstrated that non-influenza respiratory viruses (NIRV) have an important contribution to the burden of SARI, with overall one third of the SARI cases showing positivity for one or more of the respiratory viruses tested (i.e., coronavirus, human metapneumovirus, rhinovirus, enterovirus, and parainfluenza virus or respiratory syncytial virus). [27][28][29] The information retrieved from the Belgian SARI network system did not only allow to evaluate the severity of these respiratory viruses against the burden of influenza but also to investigate the vaccine efficacy and epidemiology of these viruses.…”

Section: Introductionmentioning

confidence: 89%

“…In Belgium, SARI surveillance exists since 2012 and consists presently of a network of six hospitals sending respiratory samples and clinical information from patients fulfilling the case definition to the National Influenza Centre. In particular, SARI surveillance has proven to be very useful to evaluate the severity of infections caused by different respiratory viruses, including influenza virus 27–30,33–37 . Our group also demonstrated that non‐influenza respiratory viruses (NIRV) have an important contribution to the burden of SARI, with overall one third of the SARI cases showing positivity for one or more of the respiratory viruses tested (i.e., coronavirus, human metapneumovirus, rhinovirus, enterovirus, and parainfluenza virus or respiratory syncytial virus) 27–29 .…”

Section: Introductionmentioning

confidence: 90%

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Genomic monitoring of SARS‐CoV‐2 variants using sentinel SARI hospital surveillance

Denayer,

Dufrasne,

Monsieurs

et al. 2023

Influenza Resp Viruses

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BackgroundTo support the COVID‐19 pandemic response, many countries, including Belgium, implemented baseline genomic surveillance (BGS) programs aiming to early detect and characterize new SARS‐CoV‐2 variants. In parallel, Belgium maintained a sentinel network of six hospitals that samples patients with severe acute respiratory infections (SARI) and integrated SARS‐CoV‐2 detection within a broader range of respiratory pathogens. We evaluate the ability of the SARI surveillance to monitor general trends and early signals of viral genetic evolution of SARS‐CoV‐2 and compare it with the BGS as a reference model.MethodsNine‐hundred twenty‐five SARS‐CoV‐2 positive samples from patients fulfilling the Belgian SARI definition between January 2020 and December 2022 were sequenced using the ARTIC Network amplicon tiling approach on a MinION platform. Weekly variant of concern (VOC) proportions and types were compared to those that were circulating between 2021 and 2022, using 96,251 sequences of the BGS.ResultsSARI surveillance allowed timely detection of the Omicron (BA.1, BA.2, BA.4, and BA.5) and Delta (B.1.617.2) VOCs, with no to 2 weeks delay according to the start of their epidemic growth in the Belgian population. First detection of VOCs B.1.351 and P.1 took longer, but these remained minor in Belgium. Omicron BA.3 was never detected in SARI surveillance. Timeliness could not be evaluated for B.1.1.7, being already major at the start of the study period.ConclusionsGenomic surveillance of SARS‐CoV‐2 using SARI sentinel surveillance has proven to accurately reflect VOCs detected in the population and provides a cost‐effective solution for long‐term genomic monitoring of circulating respiratory viruses.

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Analyzing infections caused by 11 respiratory pathogens in children: Pre‐ and post‐COVID‐19 pandemic trends in China

Li,

yang,

Tao

et al. 2024

Journal of Medical Virology

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With the lifting of coronavirus disease 2019 (COVID‐19) restrictions in December 2022 in China, the population was widely infected with COVID‐19. We aim to analyzed changes in the epidemiological characteristics of other respiratory pathogens in children before and after the COVID‐19 pandemic. We conducted a retrospective analysis of 44 704 children with acute respiratory infections who underwent 11 respiratory pathogen tests based on multiplex polymerase chain reaction between February and December in both 2022 and 2023. The total pathogen detection rate (24861, 74.80% vs. 6423, 56.01%; p = 0.000) and detection rates of coinfection (4059, 12.21% vs. 676, 5.89%; p = 0.000) in 2023 was significantly higher than that in 2022. The detection rates of influenza A (2567, 7.72% vs. 222, 1.94%; p = 0.000), influenza B (383, 1.15% vs. 37, 0.32%; p = 0.000), human parainfluenza virus (2175, 6.54% vs. 602, 5.25%; p = 0.000), human metapneumovirus (1354, 4.07% vs. 346, 3.01%; p = 0.000), respiratory syncytial virus (3148, 9.47% vs. 870, 7.59%; p = 0.000), and Mycoplasma pneumonia (MP; 9494, 28.56% vs. 1790, 15.61%; p = 0.000) in 2023 were significantly higher than those in 2022, whereas the detection rates of human adenovirus (1124, 3.38% vs. 489, 4.26%; p = 0.000) and human bocavirus (629, 1.89% vs. 375, 3.27%; p = 0.000) were significantly lower than those in 2022. Chlamydia, human rhinovirus, and human coronavirus showed similar detection rates between 2023 and 2022. In 2023, the influenza virus and human parainfluenza virus regained seasonal characteristic, an outbreak of MP infection occurred, the epidemic season of respiratory syncytial virus changed, and the proportion of children with acute respiratory infection aged 0–28 days and over 3 years old increased. Influenza B, metapneumovirus, and human bocavirus were detected in children aged 0–28 days in 2023, but not in 2022. After the COVID‐19 pandemic, we should be alert to the increase of respiratory diseases and the change of epidemic season and susceptible age.

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Adapting an integrated acute respiratory infections sentinel surveillance to the COVID-19 pandemic requirements, Egypt, 2020–2022

Cited by 5 publications

References 23 publications

Resurgence of influenza and respiratory syncytial virus in Egypt following two years of decline during the COVID-19 pandemic: outpatient clinic survey of infants and children, October 2022

Resurgence of influenza and respiratory syncytial virus in Egypt following two years of decline during the COVID-19 pandemic: outpatient clinic survey of infants and children, October 2022

Genomic monitoring of SARS‐CoV‐2 variants using sentinel SARI hospital surveillance

Analyzing infections caused by 11 respiratory pathogens in children: Pre‐ and post‐COVID‐19 pandemic trends in China

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