| Title |
Unlocking pandemic potential: prevalence and spatial patterns of key substitutions in avian influenza H5N1 in Egyptian isolates
|
|---|---|
| Published in |
BMC Infectious Diseases, July 2018
|
| DOI | 10.1186/s12879-018-3222-6 |
| Pubmed ID | |
| Authors |
Sean G. Young, Andrew Kitchen, Ghazi Kayali, Margaret Carrel |
| Abstract |
Avian 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. Using 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. A 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. KS 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. |
X Demographics
The data shown below were collected from the profiles of 6 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 2 | 33% |
| Egypt | 1 | 17% |
| Saudi Arabia | 1 | 17% |
| Venezuela, Bolivarian Republic of | 1 | 17% |
| Unknown | 1 | 17% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 4 | 67% |
| Practitioners (doctors, other healthcare professionals) | 1 | 17% |
| Scientists | 1 | 17% |
Mendeley readers
The data shown below were compiled from readership statistics for 34 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 34 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Master | 11 | 32% |
| Researcher | 7 | 21% |
| Student > Bachelor | 2 | 6% |
| Other | 2 | 6% |
| Lecturer | 1 | 3% |
| Other | 4 | 12% |
| Unknown | 7 | 21% |
| Readers by discipline | Count | As % |
|---|---|---|
| Medicine and Dentistry | 4 | 12% |
| Immunology and Microbiology | 4 | 12% |
| Agricultural and Biological Sciences | 4 | 12% |
| Nursing and Health Professions | 4 | 12% |
| Social Sciences | 3 | 9% |
| Other | 7 | 21% |
| Unknown | 8 | 24% |
Attention Score in Context
This research output has an Altmetric Attention Score of 19. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 31 July 2018.
All research outputs
#1,667,763
of 23,094,276 outputs
Outputs from BMC Infectious Diseases
#425
of 7,751 outputs
Outputs of similar age
#37,203
of 327,716 outputs
Outputs of similar age from BMC Infectious Diseases
#10
of 160 outputs
Altmetric has tracked 23,094,276 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 92nd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 7,751 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 10.3. This one has done particularly well, scoring higher than 94% of its peers.
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We're also able to compare this research output to 160 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 93% of its contemporaries.