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1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

Overview of attention for article published in Nature, October 2016
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  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (99th percentile)
  • High Attention Score compared to outputs of the same age and source (99th percentile)

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mendeley
225 Mendeley
citeulike
3 CiteULike
Title
1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America
Published in
Nature, October 2016
DOI 10.1038/nature19827
Pubmed ID
Authors

Michael Worobey, Thomas D. Watts, Richard A. McKay, Marc A. Suchard, Timothy Granade, Dirk E. Teuwen, Beryl A. Koblin, Walid Heneine, Philippe Lemey, Harold W. Jaffe, Worobey, Michael, Watts, Thomas D, McKay, Richard A, Suchard, Marc A, Granade, Timothy, Teuwen, Dirk E, Koblin, Beryl A, Heneine, Walid, Lemey, Philippe, Jaffe, Harold W

Abstract

The emergence of HIV-1 group M subtype B in North American men who have sex with men was a key turning point in the HIV/AIDS pandemic. Phylogenetic studies have suggested cryptic subtype B circulation in the United States (US) throughout the 1970s and an even older presence in the Caribbean. However, these temporal and geographical inferences, based upon partial HIV-1 genomes that postdate the recognition of AIDS in 1981, remain contentious and the earliest movements of the virus within the US are unknown. We serologically screened >2,000 1970s serum samples and developed a highly sensitive approach for recovering viral RNA from degraded archival samples. Here, we report eight coding-complete genomes from US serum samples from 1978-1979-eight of the nine oldest HIV-1 group M genomes to date. This early, full-genome 'snapshot' reveals that the US HIV-1 epidemic exhibited extensive genetic diversity in the 1970s but also provides strong evidence for its emergence from a pre-existing Caribbean epidemic. Bayesian phylogenetic analyses estimate the jump to the US at around 1970 and place the ancestral US virus in New York City with 0.99 posterior probability support, strongly suggesting this was the crucial hub of early US HIV/AIDS diversification. Logistic growth coalescent models reveal epidemic doubling times of 0.86 and 1.12 years for the US and Caribbean, respectively, suggesting rapid early expansion in each location. Comparisons with more recent data reveal many of these insights to be unattainable without archival, full-genome sequences. We also recovered the HIV-1 genome from the individual known as 'Patient 0' (ref. 5) and found neither biological nor historical evidence that he was the primary case in the US or for subtype B as a whole. We discuss the genesis and persistence of this belief in the light of these evolutionary insights.

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Mendeley readers

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Geographical breakdown

Country Count As %
United States 7 3%
France 3 1%
Canada 3 1%
United Kingdom 3 1%
Germany 2 <1%
Brazil 2 <1%
Japan 2 <1%
Uganda 1 <1%
Italy 1 <1%
Other 5 2%
Unknown 196 87%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 51 23%
Researcher 51 23%
Student > Master 31 14%
Student > Bachelor 30 13%
Student > Postgraduate 14 6%
Other 48 21%
Readers by discipline Count As %
Agricultural and Biological Sciences 86 38%
Biochemistry, Genetics and Molecular Biology 38 17%
Medicine and Dentistry 32 14%
Immunology and Microbiology 18 8%
Unspecified 10 4%
Other 41 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 2123. 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 May 2017.
All research outputs
#284
of 8,418,826 outputs
Outputs from Nature
#71
of 48,101 outputs
Outputs of similar age
#17
of 247,737 outputs
Outputs of similar age from Nature
#3
of 1,041 outputs
Altmetric has tracked 8,418,826 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 99th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 48,101 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 74.9. This one has done particularly well, scoring higher than 99% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 247,737 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 99% of its contemporaries.
We're also able to compare this research output to 1,041 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 99% of its contemporaries.