#Management of patients with #liver #derangement during the #COVID19 pandemic: an #Asia-Pacific position #statement (Lancet Gastroenterol Hepatol., abstract)

[Source: Lancet Gastroenterology and Hepatology, full page: (LINK). Abstract, edited.]

Management of patients with liver derangement during the COVID-19 pandemic: an Asia-Pacific position statement

Grace Lai-Hung Wong, MBChB, Prof Vincent Wai-Sun Wong, MBChB, Alex Thompson, MBBS, Prof Jidong Jia, MD, Prof Jinlin Hou, MD, Cosmas Rinaldi Adithya Lesmana, MD, Adityo Susilo, MD, Prof Yasuhito Tanaka, MD, Prof Wah-Kheong Chan, PhD, Prof Ed Gane, MD, Arlinking K Ong-Go, MD, Prof Seng-Gee Lim, MBBS, Prof Sang Hoon Ahn, MD, Prof Ming-Lung Yu, MD, Teerha Piratvisuth, MD, Prof Henry Lik-Yuen Chan, MD on behalf of the Asia-Pacific Working Group for Liver Derangement during the COVID-19 Pandemic

Published: June 22, 2020 | DOI: https://doi.org/10.1016/S2468-1253(20)30190-4



The COVID-19 pandemic has spread rapidly worldwide. It is common to encounter patients with COVID-19 with abnormal liver function, either in the form of hepatitis, cholestasis, or both. The clinical implications of liver derangement might be variable in different clinical scenarios. With growing evidence of its clinical significance, it would be clinically helpful to provide practice recommendations for various common clinical scenarios of liver derangement during the COVID-19 pandemic. The Asia-Pacific Working Group for Liver Derangement during the COVID-19 Pandemic was formed to systematically review the literature with special focus on the clinical management of patients who have been or who are at risk of developing liver derangement during this pandemic. Clinical scenarios covering the use of pharmacological treatment for COVID-19 in the case of liver derangement, and assessment and management of patients with chronic hepatitis B or hepatitis C, non-alcoholic fatty liver disease, liver cirrhosis, and liver transplantation during the pandemic are discussed.

Keywords: SARS-CoV-2; COVID-19; Hepatology.


#Work-related #COVID19 #transmission in six #Asian #countries/areas: A follow-up study (PLOS One, abstract)

[Source: PLOS One, full page: (LINK). Abstract, edited.]


Work-related COVID-19 transmission in six Asian countries/areas: A follow-up study

Fan-Yun Lan, Chih-Fu Wei, Yu-Tien Hsu, David C. Christiani, Stefanos N. Kales

Published: May 19, 2020 | DOI: https://doi.org/10.1371/journal.pone.0233588




There is limited evidence of work-related transmission in the emerging coronaviral pandemic. We aimed to identify high-risk occupations for early coronavirus disease 2019 (COVID-19) local transmission.


In this observational study, we extracted confirmed COVID-19 cases from governmental investigation reports in Hong Kong, Japan, Singapore, Taiwan, Thailand, and Vietnam. We followed each country/area for 40 days after its first locally transmitted case, and excluded all imported cases. We defined a possible work-related case as a worker with evidence of close contact with another confirmed case due to work, or an unknown contact history but likely to be infected in the working environment (e.g. an airport taxi driver). We calculated the case number for each occupation, and illustrated the temporal distribution of all possible work-related cases and healthcare worker (HCW) cases. The temporal distribution was further defined as early outbreak (the earliest 10 days of the following period) and late outbreak (11th to 40th days of the following period).


We identified 103 possible work-related cases (14.9%) among a total of 690 local transmissions. The five occupation groups with the most cases were healthcare workers (HCWs) (22%), drivers and transport workers (18%), services and sales workers (18%), cleaning and domestic workers (9%) and public safety workers (7%). Possible work-related transmission played a substantial role in early outbreak (47.7% of early cases). Occupations at risk varied from early outbreak (predominantly services and sales workers, drivers, construction laborers, and religious professionals) to late outbreak (predominantly HCWs, drivers, cleaning and domestic workers, police officers, and religious professionals).


Work-related transmission is considerable in early COVID-19 outbreaks, and the elevated risk of infection was not limited to HCW. Implementing preventive/surveillance strategies for high-risk working populations is warranted.


Citation: Lan F-Y, Wei C-F, Hsu Y-T, Christiani DC, Kales SN (2020) Work-related COVID-19 transmission in six Asian countries/areas: A follow-up study. PLoS ONE 15(5): e0233588. https://doi.org/10.1371/journal.pone.0233588

Editor: Jeffrey Shaman, Columbia University, UNITED STATES

Received: April 3, 2020; Accepted: May 8, 2020; Published: May 19, 2020

Copyright: © 2020 Lan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript and its Supporting Information files.

Funding: The authors received no specific funding for this work.

Competing interests: The authors have declared that no competing interests exist.

Keywords: SARS-CoV-2; COVID-19.


#PanStop: a decade of rapid #containment #exercises for #pandemic #preparedness in the #WHO Western #Pacific Region (Western Pac Surveill Response J., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Western Pac Surveill Response J. 2018 Winter; 9(5 Suppl 1): 71–74. Published online 2018 Dec 18. doi: 10.5365/wpsar.2018.9.5.012 | PMCID: PMC6902655

PanStop: a decade of rapid containment exercises for pandemic preparedness in the WHO Western Pacific Region

Edna Moturi,a Katherine Horton,a Leila Bell,a Lucy Breakwell,a and Erica Dueger a,b

Author information: {a} WHO Regional Office for the Western Pacific, Manila, Philippines. {b} Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States of America.

Correspondence to Erica Dueger (email: tni.ohw@raspw)

Copyright (c) 2018 The authors; licensee World Health Organization.

This is an open access article distributed under the terms of the Creative Commons Attribution IGO License (http://creativecommons.org/licenses/by/3.0/igo/legalcode), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In any reproduction of this article there should not be any suggestion that WHO or this article endorse any specific organization or products. The use of the WHO logo is not permitted. This notice should be preserved along with the article’s original URL.



Rapid containment (RC) is one of the five priority interventions of the World Health Organization (WHO) Strategic Action Plan for Pandemic Influenza; (1) it relies on the concept that mass prophylactic administration of antiviral drugs, combined with quarantine and social distancing measures, could contain or delay the international spread of an emerging influenza virus. (2, 3) During a RC operation, mass antiviral prophylaxis treatment and non-pharmaceutical interventions are rapidly implemented within a containment zone surrounding the initial cases; active surveillance and additional activities are extended to a broader buffer zone where cases are most likely to appear based on the movements of cases and contacts. (2, 4) The strategy is dependent on the rapid (within three to five days) detection, investigation and reporting of initial cases; the efficacy and availability of antivirals and vaccines; and timely risk assessment and decision-making. In the Western Pacific Region, a stockpile of antiviral medication and personal protective equipment acquired through donations from the Government of Japan is warehoused in Singapore under the auspices of the Association of South-eastern Asian Nations (ASEAN), (5) and is managed under contract by the Japan International Cooperation System (JICS). (5) These supplies are reserved for early intervention when initial signs of increased human-to-human transmission of a highly contagious influenza virus occur.


Keywords: Pandemic Influenza; Pandemic Preparedness; Antivirals; Asia Region; WHO.


#Preparedness for #influenza #vaccination during a #pandemic in the #WHO Western #Pacific Region (Western Pac Surveill Response J., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Western Pac Surveill Response J. 2018 Winter; 9(5 Suppl 1): 11–14. Published online 2018 Dec 20. doi: 10.5365/wpsar.2018.9.5.001 | PMCID: PMC6902652

Preparedness for influenza vaccination during a pandemic in the World Health Organization Western Pacific Region

Leila Bell,a Lisa Peters,a James D Heffelfinger,a Sheena G Sullivan,b,c Alba Vilajeliu,a Jinho Shin,a Joseph Bresee,d and Erica Dueger a,d

Author information: {a} WHO Regional Office for the Western Pacific, Emerging Diseases Surveillance and Response. {b} WHO Collaborating Centre for Reference and Research on Influenza at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia. {c} Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia. {d} Centers for Disease Control and Prevention, Atlanta, Georgia.

Corresponding author: Erica Dueger (email: tni.ohw@raspw)

Copyright (c) 2018 The authors; licensee World Health Organization.

This is an open access article distributed under the terms of the Creative Commons Attribution IGO License (http://creativecommons.org/licenses/by/3.0/igo/legalcode), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In any reproduction of this article there should not be any suggestion that WHO or this article endorse any specific organization or products. The use of the WHO logo is not permitted. This notice should be preserved along with the article’s original URL.



Influenza vaccination is a key public health intervention for pandemic influenza as it can limit the burden of disease, especially in high-risk groups, minimize social disruption and reduce economic impact. (1) In the event of an influenza pandemic, large-scale production, distribution and administration of pandemic vaccines in the shortest time possible is required. In addition, monitoring vaccine effectiveness, coverage and adverse events following immunization (AEFI) is important. Since seasonal influenza vaccination programmes require annual planning in each of these areas, establishing and strengthening annual influenza programmes will contribute to pandemic preparedness. (2) This paper presents efforts made in the World Health Organization (WHO) Western Pacific Region to improve seasonal influenza vaccination and pandemic preparedness.


Keywords: Pandemic Influenza; Pandemic preparedness; Vaccines; WHO; Asia Region.


Characterization and #Phylodynamics of #Reassortant #H12Nx Viruses in Northern #Eurasia (Microorganisms, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Microorganisms. 2019 Dec 3;7(12). pii: E643. doi: 10.3390/microorganisms7120643.

Characterization and Phylodynamics of Reassortant H12Nx Viruses in Northern Eurasia.

Sharshov K1, Mine J2, Sobolev I1, Kurskaya O1, Dubovitskiy N1, Kabilov M3, Alikina T3, Nakayama M2, Tsunekuni R2, Derko A1, Prokopyeva E1, Alekseev A1, Shchelkanov M4,5,6, Druzyaka A7, Gadzhiev A8, Uchida Y2, Shestopalov A1, Saito T2.

Author information: 1 Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia. 2 Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan. 3 Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia. 4 School of Biomedicine, Far Eastern Federal University, Vladivostok 690091, Russia. 5 Laboratory of Virology, Federal Scientific Center of East Asia Terrestrial Biodiversity, Vladivostok 690022, Russia. 6 Laboratory of marine microbiota, National Scientific Center o Marine Biology, Vladivostok, Vladivostok 690041, Russia. 7 Laboratory of behavioral ecology, Institute of Animal Systematics and Ecology, Novosibirsk 630091, Russia. 8 Department of ecology, Dagestan State University, Makhachkala 367000, Russia.



Wild waterfowl birds are known to be the main reservoir for a variety of avian influenza viruses of different subtypes. Some subtypes, such as H2Nx, H8Nx, H12Nx, and H14Nx, occur relatively rarely in nature. During 10-year long-term surveillance, we isolated five rare H12N5 and one H12N2 viruses in three different distinct geographic regions of Northern Eurasia and studied their characteristics. H12N2 from the Far East region was a double reassortant containing hemagglutinin (HA), non-structural (NS) and nucleoprotein (NP) segments of the American lineage and others from the classical Eurasian avian-like lineage. H12N5 viruses contain Eurasian lineage segments. We suggest a phylogeographical scheme for reassortment events associated with geographical groups of aquatic birds and their migration flyways. The H12N2 virus is of particular interest as this subtype has been found in common teal in the Russian Far East region, and it has a strong relation to North American avian influenza virus lineages, clearly showing that viral exchange of segments between the two continents does occur. Our results emphasize the importance of Avian Influenza Virus (AIV) surveillance in Northern Eurasia for the annual screening of virus characteristics, including the genetic constellation of rare virus subtypes, to understand the evolutionary ecology of AIV.

KEYWORDS: American lineage; H12Nx; Northern Eurasia; avian influenza; multiple reassortant; rare subtype; wild birds

PMID: 31816947 DOI: 10.3390/microorganisms7120643

Keywords: Avian Influenza; H12N2; H12N5; Wild Birds; Asian Region; Reassortant strain.


The #Pattern of Highly Pathogenic #Avian #Influenza #H5N1 #Outbreaks in South #Asia (Trop Med Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Trop Med Infect Dis. 2019 Nov 27;4(4). pii: E138. doi: 10.3390/tropicalmed4040138.

The Pattern of Highly Pathogenic Avian Influenza H5N1 Outbreaks in South Asia.

Chowdhury S1, Hossain ME1, Ghosh PK1, Ghosh S1, Hossain MB1, Beard C2, Rahman M1, Rahman MZ1.

Author information: 1 International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1213, Bangladesh. 2 Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA.



Highly pathogenic avian influenza (HPAI) H5N1 has caused severe illnesses in poultry and in humans. More than 15,000 outbreaks in domestic birds from 2005 to 2018 and 861 human cases from 2003 to 2019 were reported across the world to OIE (Office International des Epizooties) and WHO (World Health Organization), respectively. We reviewed and summarized the spatial and temporal distribution of HPAI outbreaks in South Asia. During January 2006 to June 2019, a total of 1063 H5N1 outbreaks in birds and 12 human cases for H5N1 infection were reported to OIE and WHO, respectively. H5N1 outbreaks were detected more in the winter season than the summer season (RR 5.11, 95% CI: 4.28-6.1). Commercial poultry were three times more likely to be infected with H5N1 than backyard poultry (RR 3.47, 95% CI: 2.99-4.01). The highest number of H5N1 outbreaks was reported in 2008, and the smallest numbers were reported in 2014 and 2015. Multiple subtypes of avian influenza viruses and multiple clades of H5N1 virus were detected. Early detection and reporting of HPAI viruses are needed to control and eliminate HPAI in South Asia.

KEYWORDS: H5N1; Highly pathogenic avian influenza viruses; South Asia; human; poultry

PMID: 31783701 DOI: 10.3390/tropicalmed4040138

Keywords: Avian Influenza; H5N1; Poultry; Asian Region.


Multiple #polymerase gene #mutations for #human #adaptation occurring in #Asian #H5N1 #influenza virus clinical isolates (Sci Rep., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Sci Rep. 2018 Aug 30;8(1):13066. doi: 10.1038/s41598-018-31397-3.

Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates.

Arai Y1,2, Kawashita N3,4, Hotta K5,6, Hoang PVM7, Nguyen HLK7, Nguyen TC7, Vuong CD7, Le TT7, Le MTQ7, Soda K8, Ibrahim MS9, Daidoji T1, Takagi T4, Shioda T2, Nakaya T1, Ito T8, Hasebe F5, Watanabe Y10,11.

Author information: 1 Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan. 2 Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan. 3 Graduate School of Science and Engineering, Kindai University, Osaka, Japan. 4 Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan. 5 Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Hanoi, Vietnam. 6 Laboratory of Veterinary Public Health, Department of Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. 7 Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam. 8 Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori, Japan. 9 Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt. 10 Department of Infectious Diseases, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan. nabe@koto.kpu-m.ac.jp. 11 Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan. nabe@koto.kpu-m.ac.jp.



The role of the influenza virus polymerase complex in host range restriction has been well-studied and several host range determinants, such as the polymerase PB2-E627K and PB2-D701N mutations, have been identified. However, there may be additional, currently unknown, human adaptation polymerase mutations. Here, we used a database search of influenza virus H5N1 clade 1.1, clade and clade 2.3.4 strains isolated from 2008-2012 in Southern China, Vietnam and Cambodia to identify polymerase adaptation mutations that had been selected in infected patients. Several of these mutations acted either alone or together to increase viral polymerase activity in human airway cells to levels similar to the PB2-D701N and PB2-E627K single mutations and to increase progeny virus yields in infected mouse lungs to levels similar to the PB2-D701N single mutation. In particular, specific mutations acted synergistically with the PB2-D701N mutation and showed synergistic effects on viral replication both in human airway cells and mice compared with the corresponding single mutations. Thus, H5N1 viruses in infected patients were able to acquire multiple polymerase mutations that acted cooperatively for human adaptation. Our findings give new insight into the human adaptation of AI viruses and help in avian influenza virus risk assessment.

PMID: 30166556 PMCID: PMC6117316 DOI: 10.1038/s41598-018-31397-3 [Indexed for MEDLINE]  Free PMC Article

Keywords: Avian Influenza; H5N1; Human; Asian Region.


Introduction of #Avian #Influenza A(#H6N5) Virus into #Asia from North #America by #WildBirds (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 11—November 2019 / Research Letter

Introduction of Avian Influenza A(H6N5) Virus into Asia from North America by Wild Birds

Sol Jeong, Dong-Hun Lee  , Yu-Jin Kim, Sun-Hak Lee, Andrew Y. Cho, Jin-Yong Noh1, Erdene-Ochir Tseren-Ochir2, Jei-Hyun Jeong, and Chang-Seon Song

Author affiliations: University of Connecticut, Storrs, Connecticut, USA (S. Jeong, D.-H. Lee); Konkuk University, Seoul, South Korea (S. Jeong, Y.-J. Kim, S.-H. Lee, A.Y. Cho, J.-Y. Noh, E.-O. Tseren-Ochir, J.-H. Jeong, C.-S. Song)



An avian influenza A(H6N5) virus with all 8 segments of North American origin was isolated from wild bird feces in South Korea. Phylogenetic analysis suggests that this virus may have been introduced into Asia by wild birds, highlighting the role of wild birds in the dispersal of these viruses.

Keywords: Avian Influenza; H6N5; Wild Birds; Asia Region.


Available #evidence of #antibiotic #resistance from #ESBL-producing #Enterobacteriaceae in #paediatric patients in 20 countries: a systematic review and meta-analysis (Bull World Health Organ., abstract)

[Source: Bulletin of the World Health Organization, full page: (LINK). Abstract, edited.]

Available evidence of antibiotic resistance from extended-spectrum β-lactamase-producing Enterobacteriaceae in paediatric patients in 20 countries: a systematic review and meta-analysis

Yanhong Jessika Hu,a, Anju Ogyu,a, Benjamin J Cowling,a, Keiji Fukuda a & Herbert H Pang a

{a} School of Public Health, Patrick Manson Building (North Wing), 7 Sassoon Road, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special
Administrative Region, China.

Correspondence to Yanhong Jessika Hu (email: huhubest@gmail.com).

Submitted: 20 October 2018 – Revised version received: 8 April 2019 – Accepted: 9 April 2019 – Published online: 14 May 2019

Bull World Health Organ 2019;97:486–501B | doi: http://dx.doi.org/10.2471/BLT.18.225698




To make a systematic review of risk factors, outcomes and prevalence of extended-spectrum β-lactamase-associated infection in children and young adults in South-East Asia and the Western Pacific.


Up to June 2018 we searched online databases for published studies of infection with extended-spectrum β-lactamase-producing Enterobacteriaceae in individuals aged 0–21 years. We included case–control, cohort, cross-sectional and observational studies reporting patients positive and negative for these organisms. For the meta-analysis we used random-effects modelling of risk factors and outcomes for infection, and meta-regression for analysis of subgroups. We mapped the prevalence of these infections in 20 countries and areas using available surveillance data.


Of 6665 articles scanned, we included 40 studies from 11 countries and areas in the meta-analysis. The pooled studies included 2411 samples testing positive and 2874 negative. A higher risk of infectionwith extended-spectrum β-lactamase-producing bacteria was associated with previous hospital care, notably intensive care unit stays (pooled odds ratio, OR: 6.5; 95% confidence interval, CI: 3.04 to 13.73); antibiotic exposure (OR: 4.8; 95% CI: 2.25 to 10.27); and certain co-existing conditions. Empirical antibiotic therapy was protective against infection (OR: 0.29; 95% CI: 0.11 to 0.79). Infected patients had longer hospital stays (26 days; 95% CI: 12.81 to 38.89) and higher risk of death (OR: 3.2; 95% CI: 1.82 to 5.80). The population prevalence of infection was high in these regions and surveillance data for children were scarce.


Antibiotic stewardship policies to prevent infection and encourage appropriate treatment are needed in South-East Asia and the Western Pacific

Keywords: Antibiotics; Drugs Resistance; Pediatrics; Asia Region.


Causes of severe #pneumonia requiring #hospital admission in #children without HIV infection from #Africa and #Asia: the #PERCH multi-country case-control study (Lancet, abstract)

[Source: The Lancet, full page: (LINK). Abstract, edited.]

Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study

The Pneumonia Etiology Research for Child Health (PERCH) Study Group †

Open Access / Published: June 27, 2019 / DOI: https://doi.org/10.1016/S0140-6736(19)30721-4




Pneumonia is the leading cause of death among children younger than 5 years. In this study, we estimated causes of pneumonia in young African and Asian children, using novel analytical methods applied to clinical and microbiological findings.


We did a multi-site, international case-control study in nine study sites in seven countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. All sites enrolled in the study for 24 months. Cases were children aged 1–59 months admitted to hospital with severe pneumonia. Controls were age-group-matched children randomly selected from communities surrounding study sites. Nasopharyngeal and oropharyngeal (NP-OP), urine, blood, induced sputum, lung aspirate, pleural fluid, and gastric aspirates were tested with cultures, multiplex PCR, or both. Primary analyses were restricted to cases without HIV infection and with abnormal chest x-rays and to controls without HIV infection. We applied a Bayesian, partial latent class analysis to estimate probabilities of aetiological agents at the individual and population level, incorporating case and control data.


Between Aug 15, 2011, and Jan 30, 2014, we enrolled 4232 cases and 5119 community controls. The primary analysis group was comprised of 1769 (41·8% of 4232) cases without HIV infection and with positive chest x-rays and 5102 (99·7% of 5119) community controls without HIV infection. Wheezing was present in 555 (31·7%) of 1752 cases (range by site 10·6–97·3%). 30-day case-fatality ratio was 6·4% (114 of 1769 cases). Blood cultures were positive in 56 (3·2%) of 1749 cases, and Streptococcus pneumoniae was the most common bacteria isolated (19 [33·9%] of 56). Almost all cases (98·9%) and controls (98·0%) had at least one pathogen detected by PCR in the NP-OP specimen. The detection of respiratory syncytial virus (RSV), parainfluenza virus, human metapneumovirus, influenza virus, S pneumoniae, Haemophilus influenzae type b (Hib), H influenzae non-type b, and Pneumocystis jirovecii in NP-OP specimens was associated with case status. The aetiology analysis estimated that viruses accounted for 61·4% (95% credible interval [CrI] 57·3–65·6) of causes, whereas bacteria accounted for 27·3% (23·3–31·6) and Mycobacterium tuberculosis for 5·9% (3·9–8·3). Viruses were less common (54·5%, 95% CrI 47·4–61·5 vs 68·0%, 62·7–72·7) and bacteria more common (33·7%, 27·2–40·8 vs 22·8%, 18·3–27·6) in very severe pneumonia cases than in severe cases. RSV had the greatest aetiological fraction (31·1%, 95% CrI 28·4–34·2) of all pathogens. Human rhinovirus, human metapneumovirus A or B, human parainfluenza virus, S pneumoniae, M tuberculosis, and H influenzae each accounted for 5% or more of the aetiological distribution. We observed differences in aetiological fraction by age for Bordetella pertussis, parainfluenza types 1 and 3, parechovirus–enterovirus, P jirovecii, RSV, rhinovirus, Staphylococcus aureus, and S pneumoniae, and differences by severity for RSV, S aureus, S pneumoniae, and parainfluenza type 3. The leading ten pathogens of each site accounted for 79% or more of the site’s aetiological fraction.


In our study, a small set of pathogens accounted for most cases of pneumonia requiring hospital admission. Preventing and treating a subset of pathogens could substantially affect childhood pneumonia outcomes.


Bill & Melinda Gates Foundation.

Keywords: Pneumonia; Pediatrics; Africa; Asia; Streptococcus pneumoniae; RSV; Metapneumovirus; Seasonal Influenza.