Evidence map›Paper›PMID 29795677›Full record

ArticlePloS one2018

Intra-host and intra-household diversity of influenza A viruses during household transmissions in the 2013 season in 2 peri-urban communities of South Africa.

Ziyaad Valley-Omar, Preetha Iyengar, Claire von Mollendorf, Stefano Tempia, Alexandra Moerdyk, Orienka Hellferscee, Neil Martinson, Meredith McMorrow, Ebrahim Variava, Katlego Masonoke and 3 more

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In one paragraph

Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

3 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Review
  3. Article
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

13 authors.

Ziyaad Valley-OmarCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.ORCID 0000-0003-4804-3774
Preetha IyengarEpidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
Claire von MollendorfCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Stefano TempiaInfluenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
Alexandra MoerdykCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Orienka HellfersceeCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Neil MartinsonPerinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Meredith McMorrowInfluenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.
Ebrahim VariavaDepartment of Internal Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.
Katlego MasonokePerinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Adam L CohenInfluenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
Cheryl CohenCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Florette K TreurnichtCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.

Funding

Research on the Epidemiology,Prevention,Vaccine Effectiveness and Treatment of Influenza and Other Respiratory Viruses in South Africa.09U01IP001048 · IP · NATIONAL HEALTH LABORATORY SERVICE · PI COHEN, CHERYL · 2016 to 2020
$19.9M
ACL HHS U19GH000622NCIRD CDC HHS U01 IP001048NCIRD CDC HHS U51 IP000528World Health Organization 001
6 · The paper itself

Abstract

Limited information is available on influenza virus sequence drift between transmission events. In countries with high HIV burdens, like South Africa, the direct and indirect effect of HIV on influenza sequence drift between transmission events may be of public health concern. To this end, we measured hemagglutinin sequence diversity between influenza transmission events using data and specimens from a study investigating household transmission dynamics of seasonal influenza viruses in 2 peri-urban communities in South Africa during the 2013 influenza season. Thirty index cases and 107 of 110 eligible household contacts were enrolled into the study, 47% (14/30) demonstrating intra-household laboratory-confirmed influenza transmission. In this study 35 partial hemagglutinin gene sequences were obtained by Sanger sequencing from 11 index cases (sampled at enrolment only) and 16 secondary cases (8 cases sampled at 1 and 8 cases sampled at 2 time-points). Viral sequence identities confirmed matched influenza transmission pairs within the 11 households with corresponding sequenced index and secondary cases. Phylogenetic analysis revealed 10 different influenza viral lineages in the 14 households. Influenza A(H1N1)pdm09 strains were shown to be genetically distinct between the 2 communities (from distinct geographic regions), which was not observed for the influenza A(H3N2) strains. Intra-host/intra-household influenza A(H3N2) sequence drift was identified in 2 households. The first was a synonymous mutation between the index case and a household contact, and the second a non-synonymous mutation between 2 serial samples taken at days 0 and 4 post enrolment from an HIV-infected secondary case. Limited inter-household sequence diversity was observed as highlighted by sharing of the same influenza strain between different households within each community. The limited intra-household sequence drift is in line with previous studies also using Sanger sequencing, corroborating the presence of strict selective bottlenecks that limit sequence variance. We were not able to directly ascertain the effect of HIV on influenza sequence drift between transmission events.

Indexed as

Family CharacteristicsGenetic VariationHemagglutinin Glycoproteins, Influenza VirusHumansInfluenza A virusInfluenza, HumanPhylogenyRisk FactorsRNA, ViralSequence Analysis, DNASouth AfricaHemagglutinin Glycoproteins, Influenza VirusRNA, Viral

Identifiers

PMID29795677
PMCPMC5967731

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Registered trials

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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.