The Epidemiology of Pathogens in Community‐Acquired Pneumonia Among Children in Southwest China Before, During and After COVID‐19 Non‐pharmaceutical Interventions: A Cross‐Sectional Study

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ABSTRACT

Objective

This study aimed to investigate the pathogen epidemiology of community‐acquired pneumonia (CAP) among children in Southwest China before, during and after the COVID‐19 non‐pharmaceutical interventions (NPIs).

Methods

Pathogen data of hospitalised children with CAP, including multiple direct immunofluorescence test for seven viruses, bacterial culture and polymerase chain reaction (PCR) for Mycoplasma pneumoniae , were analysed across three phases: Phase I (pre‐NPIs: 1 January 2019 to 31 December 2019), Phase II (NPI period: 1 January 2020 to 31 December 2020) and Phase III (post‐NPIs: 1 January 2023 to 31 December 2023).

Results

A total of 7533 cases were enrolled, including 2444, 1642 and 3447 individuals in Phases I, II and III, respectively. M. pneumoniae predominated in Phases I and III (23.4% and 35.5%, respectively). In Phase II, respiratory syncytial virus (RSV) emerged as the primary pathogen (20.3%), whereas detection rates of influenza A virus (Flu A) and M. pneumoniae were at a low level (1.8% and 9.6%, respectively). In Phase III, both Flu A (15.8%) and M. pneumoniae epidemic rebounded, whereas RSV detection rate returned to Phase I level, and detection rates of Streptococcus pneumoniae and Haemophilus influenzae decreased significantly compared to those in Phase I. Detection rates of adenovirus and parainfluenza virus type 3 decreased phase by phase. Age‐stratified analysis and monthly variations supported the above findings. Seasonal patterns of multiple pathogens were disrupted during Phases II and III.

Conclusions

COVID‐19 NPIs exhibited a distinct impact on CAP pathogen epidemic among children, with post‐NPIs increases observed in M. pneumoniae and Flu A prevalence. Continuous pathogen monitoring is crucial for effective prevention and control of paediatric CAP.

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Most cited references 27

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Coronavirus Disease 2019 (COVID-19): A Perspective from China

Zi Yue Zu, Meng Jiang, Peng Xu … (2020)

Abstract In December 2019, an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection occurred in Wuhan, Hubei Province, China and spread across China and beyond. On February 12, 2020, WHO officially named the disease caused by the novel coronavirus as Coronavirus Disease 2019 (COVID-19). Since most COVID-19 infected patients were diagnosed with pneumonia and characteristic CT imaging patterns, radiological examinations have become vital in early diagnosis and assessment of disease course. To date, CT findings have been recommended as major evidence for clinical diagnosis of COVID-19 in Hubei, China. This review focuses on the etiology, epidemiology, and clinical symptoms of COVID-19, while highlighting the role of chest CT in prevention and disease control. A full translation of this article in Chinese is available in the supplement. - 请见䃼充资料阅读文章中文版∘

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Estimating excess mortality due to the COVID-19 pandemic: a systematic analysis of COVID-19-related mortality, 2020–21

(2022)

Background Mortality statistics are fundamental to public health decision making. Mortality varies by time and location, and its measurement is affected by well known biases that have been exacerbated during the COVID-19 pandemic. This paper aims to estimate excess mortality from the COVID-19 pandemic in 191 countries and territories, and 252 subnational units for selected countries, from Jan 1, 2020, to Dec 31, 2021. Methods All-cause mortality reports were collected for 74 countries and territories and 266 subnational locations (including 31 locations in low-income and middle-income countries) that had reported either weekly or monthly deaths from all causes during the pandemic in 2020 and 2021, and for up to 11 year previously. In addition, we obtained excess mortality data for 12 states in India. Excess mortality over time was calculated as observed mortality, after excluding data from periods affected by late registration and anomalies such as heat waves, minus expected mortality. Six models were used to estimate expected mortality; final estimates of expected mortality were based on an ensemble of these models. Ensemble weights were based on root mean squared errors derived from an out-of-sample predictive validity test. As mortality records are incomplete worldwide, we built a statistical model that predicted the excess mortality rate for locations and periods where all-cause mortality data were not available. We used least absolute shrinkage and selection operator (LASSO) regression as a variable selection mechanism and selected 15 covariates, including both covariates pertaining to the COVID-19 pandemic, such as seroprevalence, and to background population health metrics, such as the Healthcare Access and Quality Index, with direction of effects on excess mortality concordant with a meta-analysis by the US Centers for Disease Control and Prevention. With the selected best model, we ran a prediction process using 100 draws for each covariate and 100 draws of estimated coefficients and residuals, estimated from the regressions run at the draw level using draw-level input data on both excess mortality and covariates. Mean values and 95% uncertainty intervals were then generated at national, regional, and global levels. Out-of-sample predictive validity testing was done on the basis of our final model specification. Findings Although reported COVID-19 deaths between Jan 1, 2020, and Dec 31, 2021, totalled 5·94 million worldwide, we estimate that 18·2 million (95% uncertainty interval 17·1–19·6) people died worldwide because of the COVID-19 pandemic (as measured by excess mortality) over that period. The global all-age rate of excess mortality due to the COVID-19 pandemic was 120·3 deaths (113·1–129·3) per 100 000 of the population, and excess mortality rate exceeded 300 deaths per 100 000 of the population in 21 countries. The number of excess deaths due to COVID-19 was largest in the regions of south Asia, north Africa and the Middle East, and eastern Europe. At the country level, the highest numbers of cumulative excess deaths due to COVID-19 were estimated in India (4·07 million [3·71–4·36]), the USA (1·13 million [1·08–1·18]), Russia (1·07 million [1·06–1·08]), Mexico (798 000 [741 000–867 000]), Brazil (792 000 [730 000–847 000]), Indonesia (736 000 [594 000–955 000]), and Pakistan (664 000 [498 000–847 000]). Among these countries, the excess mortality rate was highest in Russia (374·6 deaths [369·7–378·4] per 100 000) and Mexico (325·1 [301·6–353·3] per 100 000), and was similar in Brazil (186·9 [172·2–199·8] per 100 000) and the USA (179·3 [170·7–187·5] per 100 000). Interpretation The full impact of the pandemic has been much greater than what is indicated by reported deaths due to COVID-19 alone. Strengthening death registration systems around the world, long understood to be crucial to global public health strategy, is necessary for improved monitoring of this pandemic and future pandemics. In addition, further research is warranted to help distinguish the proportion of excess mortality that was directly caused by SARS-CoV-2 infection and the changes in causes of death as an indirect consequence of the pandemic. Funding Bill & Melinda Gates Foundation, J Stanton, T Gillespie, and J and E Nordstrom

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Is Open Access

The Novel Coronavirus: A Bird's Eye View

Parham Habibzadeh, Emily K Stoneman (2020)

The novel coronavirus (2019-nCoV) outbreak, which initially began in China, has spread to many countries around the globe, with the number of confirmed cases increasing every day. With a death toll exceeding that of the SARS-CoV outbreak back in 2002 and 2003 in China, 2019-nCoV has led to a public health emergency of international concern, putting all health organizations on high alert. Herein, we present on an overview of the currently available information on the pathogenesis, epidemiology, clinical presentation, diagnosis, and treatment of this virus.

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Author and article information

Contributors

Xiaoying Wu:

ORCID: https://orcid.org/0000-0001-5457-4462

wuxiaoying428@163.com

Journal

Journal ID (nlm-ta): Influenza Other Respir Viruses

Journal ID (iso-abbrev): Influenza Other Respir Viruses

Journal ID (doi): 10.1111/(ISSN)1750-2659

Journal ID (publisher-id): IRV

Title: Influenza and Other Respiratory Viruses

Publisher: John Wiley and Sons Inc. (Hoboken )

ISSN (Print): 1750-2640

ISSN (Electronic): 1750-2659

Publication date (Electronic): 15 August 2024

Publication date Collection: August 2024

Volume: 18

Issue: 8 ( doiID: 10.1111/irv.v18.8 )

Electronic Location Identifier: e13361

Affiliations

[ ¹ ] Department of Infectious Diseases Children's Hospital of Chongqing Medical University Chongqing China

[ ² ] National Clinical Research Center for Child Health and Disorders Ministry of Education Key Laboratory of Child Development and Disorders Chongqing China

[ ³ ] The First Batch of Key Disciplines on Public Health in Chongqing Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity Chongqing China

Author information

Xiaoying Wu https://orcid.org/0000-0001-5457-4462

Article

Publisher ID: IRV13361 Other ID: IRV-2024-147.R2

DOI: 10.1111/irv.13361

PMC ID: 11325253

PubMed ID: 39145530

SO-VID: 0b2ef174-d622-4781-a628-edd4a853b56d

License:

This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

History

Date revision received : 25 July 2024

Date received : 08 April 2024

Date accepted : 26 July 2024

Page count

Figures: 3, Tables: 1, Pages: 9, Words: 6300

Custom metadata

source-schema-version-number 2.0

cover-date August 2024

details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:6.4.6 mode:remove_FC converted:15.08.2024

ScienceOpen disciplines: Infectious disease & Microbiology

Keywords: community‐acquired pneumonia,covid‐19,influenza virus, mycoplasma pneumoniae ,paediatric,pathogen epidemiology

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ScienceOpen disciplines: Infectious disease & Microbiology

Keywords: community‐acquired pneumonia, covid‐19, influenza virus, mycoplasma pneumoniae , paediatric, pathogen epidemiology

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The Epidemiology of Pathogens in Community‐Acquired Pneumonia Among Children in Southwest China Before, During and After COVID‐19 Non‐pharmaceutical Interventions: A Cross‐Sectional Study

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Novel Coronavirus Disease COVID-19

Most cited references 27

Coronavirus Disease 2019 (COVID-19): A Perspective from China

Estimating excess mortality due to the COVID-19 pandemic: a systematic analysis of COVID-19-related mortality, 2020–21

The Novel Coronavirus: A Bird's Eye View

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