Evidence map›Paper›PMID 29980172›Full record

ArticleBMC infectious diseases2018

Unlocking pandemic potential: prevalence and spatial patterns of key substitutions in avian influenza H5N1 in Egyptian isolates.

Sean G Young, Andrew Kitchen, Ghazi Kayali, Margaret Carrel

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC infectious diseases, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
0.5field-weighted citation impact, top 33% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed, 9 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors at 3 institutions in 1 country.

Sean G YoungDepartment of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA. SGYoung@uams.edu.ORCID 0000-0002-0054-0627
Andrew KitchenDepartment of Anthropology, University of Iowa, Iowa City, IA, USA.
Ghazi KayaliDepartment of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Sciences Center, Houston, TX, USA.
Margaret CarrelDepartment of Geographical and Sustainability Sciences, University of Iowa, Iowa City, IA, USA.
University of Iowa · USThe University of Texas Health Science Center at Houston · USUniversity of Arkansas Medical Center · US

Funding

National Institute of Allergy and Infectious Diseases DMID contract HHSN272201400006CNational Science Foundation 0966130NIAID NIH HHS HHSN272201400006C
6 · The paper itself

Abstract

backgroundAvian influenza H5N1 has a high human case fatality rate, but is not yet well-adapted to human hosts. Amino acid substitutions currently circulating in avian populations may enhance viral fitness in, and thus viral adaptation to, human hosts. Substitutions which could increase the risk of a human pandemic (through changes to host specificity, virulence, replication ability, transmissibility, or drug susceptibility) are termed key substitutions (KS). Egypt represents the epicenter of human H5N1 infections, with more confirmed cases than any other country. To date, however, there have not been any spatial analyses of KS in Egypt.

methodsUsing 925 viral samples of H5N1 from Egypt, we aligned protein sequences and scanned for KS. We geocoded isolates using dasymetric mapping, then carried out geospatial hot spot analyses to identify spatial clusters of high KS detection rates. KS prevalence and spatial clusters were evaluated for all detected KS, as well as when stratified by phenotypic consequence.

resultsA total of 39 distinct KS were detected in the wild, including 17 not previously reported in Egypt. KS were detected in 874 samples (94.5%). Detection rates varied by viral protein with most KS observed in the surface hemagglutinin (HA) and neuraminidase (NA) proteins, as well as the interior non-structural 1 (NS1) protein. The most frequently detected KS were associated with increased viral binding to mammalian cells and virulence. Samples with high overall detection rates of KS exhibited statistically significant spatial clustering in two governorates in the northwestern Nile delta, Alexandria and Beheira.

conclusionsKS provide a possible mechanism by which avian influenza H5N1 could evolve into a pandemic candidate. With numerous KS circulating in Egypt, and non-random spatial clustering of KS detection rates, these findings suggest the need for increased surveillance in these areas.

Indexed as

Amino Acid SubstitutionAnimalsBirdsEgyptHemagglutininsInfluenza A Virus, H5N1 SubtypeInfluenza in BirdsNeuraminidasePandemicsPrevalenceViral ProteinsHemagglutininsNeuraminidaseViral ProteinsAvian influenzaEgyptLandscape geneticsPoultry

Identifiers

PMID29980172
PMCPMC6035396
OpenAlexW2828265528

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.