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| Open AccessRisk of COVID-19 death in adults who received booster COVID-19 vaccinations in England
Ward et al. utilise electronic health records to identify groups of adults (who had received a second booster dose of a COVID-19 vaccine) at elevated risk of COVID-19 death.
- Isobel L. Ward
- , Chris Robertson
- & Vahé Nafilyan
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Article
| Open AccessWastewater sequencing reveals community and variant dynamics of the collective human virome
Tisza et al. carry out a sequencing-based analysis of wastewater samples from major cities, to detect and quantify hundreds of distinct pathogenic viruses, finding striking correlations between virus abundance and local clinical cases.
- Michael Tisza
- , Sara Javornik Cregeen
- & Anthony W. Maresso
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Article
| Open AccessSpatial and temporal dynamics of West Nile virus between Africa and Europe
West Nile virus is an animal pathogen that has spread rapidly in Europe in recent years, causing several human deaths. This study investigates the spatial and temporal dynamics of the virus circulation between Africa (its place of origin) and Europe.
- Giulia Mencattelli
- , Marie Henriette Dior Ndione
- & Giovanni Savini
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| Open AccessIncreased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil
Chikungunya virus is endemic in Brazil and cases have been rapidly increasing in recent years. Here, the authors describe the expansion of a genomic surveillance program across the country allowing them to characterise the emergence and dispersal of two distinct subclades mainly seeded from the north eastern region.
- Joilson Xavier
- , Luiz Carlos Junior Alcantara
- & Marta Giovanetti
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| Open AccessHighly lethal genotype I and II recombinant African swine fever viruses detected in pigs
Potential recombination of African swine fever virus genotypes is not well understood. Here, Zhao et al. report naturally occurring ASFVs carrying mosaic genomes of genotype I and II and show that the recombinant virus is lethal in pigs and evades the immunity induced by genotype II live vaccine.
- Dongming Zhao
- , Encheng Sun
- & Zhigao Bu
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| Open AccessVirus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals
Monitoring the diversity of viruses infecting animals is important for assessing zoonotic risk. Here, the authors use metatranscriptomics to characterise the viromes of small mammals, pangolins, and zoo animals in China to identify potentially zoonotic viruses.
- Xinyuan Cui
- , Kewei Fan
- & Yongyi Shen
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| Open AccessComparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas
The Amazonas region has been the most heavily affected by COVID-19 in Brazil. In this study, the authors conduct phylodynamic analyses to assess SARS-CoV-2 lineage replacement dynamics in the region and infer the impact of population immunity on the spread and severity of the Delta and Omicron variants.
- Ighor Arantes
- , Gonzalo Bello
- & Felipe Gomes Naveca
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| Open AccessEmergence and spread of two SARS-CoV-2 variants of interest in Nigeria
Data on geographically restricted SARS-CoV-2 variants is lacking in some regions. In this nationwide effort including 18 public health labs, the authors used genomic epidemiology and travel data to understand the origin and spread of 2 variants of interest that predominated during the second wave of the pandemic in Nigeria.
- Idowu B. Olawoye
- , Paul E. Oluniyi
- & Christian T. Happi
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Article
| Open AccessSeroepidemiology of enterovirus A71 infection in prospective cohort studies of children in southern China, 2013-2018
Hand, foot and mouth disease, caused by enterovirus A71 (EV-A71) infection, is common in children in China. Here, the authors estimate EV-A71 incidence and seroprevalence using data from two longitudinal cohorts and find that, despite high infection rates, a large proportion of children under 6 are susceptible.
- Juan Yang
- , Qiaohong Liao
- & Hongjie Yu
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Article
| Open AccessHuman infection with a reassortment avian influenza A H3N8 virus: an epidemiological investigation study
The H3N8 influenza virus is known to circulate in wild birds but cross-species transmission to mammalian hosts was also reported. In this case study, the authors report human infection with a reassortment avian influenza A H3N8 virus in a four-year old boy that developed severe symptoms.
- Pengtao Bao
- , Yang Liu
- & Wei Liu
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| Open AccessDynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England
The REACT-1 study measures the community prevalence of SARS-CoV-2 in England through repeated cross-sectional surveys. Here, the authors present data from REACT-1 that document the increase in infection prevalence, particularly among children, associated with the Omicron variant in January 2022.
- Paul Elliott
- , Oliver Eales
- & Christl A. Donnelly
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Article
| Open AccessTransmission of SARS-CoV-2 from humans to animals and potential host adaptation
Here, Tan et al. find that the rapid spread of SARS-CoV-2 in mink and deer required minimal adaptation, has only caused moderate changes to the evolutionary trajectory of the virus, and has not led to viral mutations that greatly improve human transmission thus far.
- Cedric C. S. Tan
- , Su Datt Lam
- & François Balloux
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Article
| Open AccessOff-season RSV epidemics in Australia after easing of COVID-19 restrictions
Non-pharmaceutical interventions for COVID-19 also reduced incidence of respiratory pathogens such as respiratory syncytial virus (RSV). Here, the authors report the resurgence of RSV in Australia following lifting of some of the restrictions and describe reduction in genetic diversity in circulating clades.
- John-Sebastian Eden
- , Chisha Sikazwe
- & Tyna Tran
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Article
| Open AccessElimination of human rabies in Goa, India through an integrated One Health approach
Dog vaccination is an effective rabies prevention measure, but widespread vaccination campaigns are challenging in settings like India with large free-roaming dog populations. Here, the authors describe a One Health campaign in Goa state which led to a large reduction of cases in dogs and elimination in humans.
- A. D. Gibson
- , G. Yale
- & R. J. Mellanby
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| Open AccessIncorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission
The time-varying effective reproductive number (Rt) is useful for monitoring transmission of infections such as COVID-19, but reporting delays impact case count-based estimation methods. Here, the authors demonstrate and validate a method for estimation of Rt based on viral load data from Hong Kong that does not require accurate daily counts.
- Yun Lin
- , Bingyi Yang
- & Benjamin J. Cowling
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Comment
| Open AccessAusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic
The COVID-19 pandemic has accelerated the demand for near real-time analysis and dissemination of pathogen genomic data. In this comment, the authors describe how Australia has developed and rolled out its SARS-CoV-2 genomics platform, AusTrakka, and used it to support public health action.
- Tuyet Hoang
- , Anders Gonçalves da Silva
- & Torsten Seemann
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| Open AccessGenomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong
Hong Kong has used an elimination strategy to control SARS-CoV-2 with stringent measures including traveller quarantine. Here, the authors show that the majority of community-acquired cases until January 2021 resulted from three importations, and that increased transmission followed prolonged periods of restrictions, likely due to adherence fatigue.
- Haogao Gu
- , Ruopeng Xie
- & Leo L. M. Poon
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Article
| Open AccessGenomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
In this study, Aggarwal and colleagues perform prospective sequencing of SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge. They identify important factors that contributed to within university transmission and onward spread into the wider community.
- Dinesh Aggarwal
- , Ben Warne
- & Ian G. Goodfellow
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| Open AccessPlasma virome and the risk of blood-borne infection in persons with substance use disorder
Spread of bloodborne infections, such as HCV and HIV, is a problem, particularly amongst people who inject drugs (PWID). Here, the authors describe and then confirm in observational PWID cohorts that those with more non-pathogenic viruses in plasma were more likely later to acquire HCV than PWID who had fewer of these non-pathogenic viruses.
- Abraham J. Kandathil
- , Andrea L. Cox
- & David L. Thomas
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| Open AccessAdaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands
SARS-CoV-2 was detected in mink farms in the Netherlands in the first wave of the pandemic with evidence of human-to-mink and mink-to-human transmission. Here, the authors investigate this outbreak using phylodynamic analysis and show that personnel links and spatial proximity are predictors of transmission between farms.
- Lu Lu
- , Reina S. Sikkema
- & Marion P. G. Koopmans
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Article
| Open AccessModel-based assessment of Chikungunya and O’nyong-nyong virus circulation in Mali in a serological cross-reactivity context
O’nyong nyong and Chikungunya virus are arboviruses present in Africa but their prevalence is unknown, partly due to high antibody cross-reactivity with one another. Here, the authors develop a statistical model that accounts for cross-reactivity to characterise circulation of both viruses from seroprevalence surveys.
- Nathanaël Hozé
- , Issa Diarra
- & Simon Cauchemez
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Article
| Open AccessFunctional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5
MERS-CoV is enzootic in dromedary camels, can spread to humans but undergoes limited onward transmission. Here, Schroeder et al. compare clinical isolates of MERS-CoV in vitro and show that the predominantly circulating recombinant lineage 5 possess a fitness advantage over parental lineage 3 and 4 due to reduced activation of innate immune signaling.
- Simon Schroeder
- , Christin Mache
- & Christian Drosten
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Article
| Open AccessSeasonality of agricultural exposure as an important predictor of seasonal yellow fever spillover in Brazil
Yellow fever virus (YFV) is an arbovirus affecting humans and non-human primates (NHPs) with seasonal transmission. Here Hamlet et al. model the monthly occurrence of YF in humans and NHPs across Brazil and show that seasonality of agriculture is an important predictor of seasonal YF transmission.
- Arran Hamlet
- , Daniel Garkauskas Ramos
- & Neil M. Ferguson
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Article
| Open AccessMolecular evidence of SARS-CoV-2 in New York before the first pandemic wave
Matthew M. Hernandez and Ana S. Gonzalez-Reiche and colleagues report evidence of SARSCoV-2 infections in respiratory pathogen-negative nasopharyngeal specimens collected in New York, which date back to over one month before the first officially documented case in the state. The findings provide insights in to the origins of the virus in New York.
- Matthew M. Hernandez
- , Ana S. Gonzalez-Reiche
- & Emilia Mia Sordillo
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Article
| Open AccessImpact of COVID-19 outbreaks and interventions on influenza in China and the United States
Non-pharmaceutical interventions (NPIs) implemented to interrupt COVID-19 transmission may also impact the spread of other infectious diseases. Here, the authors estimate that influenza activity in China and the United States reduced by up to 80% when NPIs were in place in the 2019–2020 season.
- Luzhao Feng
- , Ting Zhang
- & George F. Gao
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Article
| Open AccessLying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
Zika and dengue incidence in the Americas declined in 2017–2018, but dengue resurged in 2019 in Brazil. This study uses epidemiological, climatological and genomic data to show that the decline of dengue may be explained by protective immunity from pre-exposure to ZIKV and/or DENV in prior years.
- Anderson Fernandes Brito
- , Lais Ceschini Machado
- & Nathan D. Grubaugh
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Article
| Open AccessInfectivity, susceptibility, and risk factors associated with SARS-CoV-2 transmission under intensive contact tracing in Hunan, China
Detailed knowledge of COVID-19 epidemiology is needed to inform public health responses. Here, the authors use large-scale contact tracing data to provide empirical estimates of key parameters, and show that susceptibility increases with age but transmissibility does not vary significantly.
- Shixiong Hu
- , Wei Wang
- & Hongjie Yu
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Article
| Open AccessRecent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains
Here, the authors compare seven low passage Zika virus (ZIKV) strains representing the recently circulating viral genetic diversity of African and Asian strains and find that African ZIKV strains have higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice.
- Fabien Aubry
- , Sofie Jacobs
- & Louis Lambrechts
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| Open AccessGenomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia
The COVID-19 epidemic began later in Russia than many European countries, possibly due to restrictions on travel from China. Here, the authors analyze whole genome sequences sampled early in the epidemic in Russia, and find that most strains were not linked to China.
- Andrey B. Komissarov
- , Ksenia R. Safina
- & Georgii A. Bazykin
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Article
| Open AccessEpidemiological hypothesis testing using a phylogeographic and phylodynamic framework
Classical epidemiological approaches have been limited in their ability to formally test hypotheses. Here, Dellicour et al. illustrate how phylodynamic and phylogeographic analyses can be leveraged for hypothesis testing in molecular epidemiology using West Nile virus in North America as an example.
- Simon Dellicour
- , Sebastian Lequime
- & Philippe Lemey
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Article
| Open AccessDeep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study
Detailed knowledge of the characteristics of COVID-19 patients helps with public health planning. Here, the authors use routinely-collected data from seven databases in three countries to describe the characteristics of >30,000 patients admitted with COVID-19 and compare them with those admitted for influenza in previous years.
- Edward Burn
- , Seng Chan You
- & Patrick Ryan
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Article
| Open AccessBroadly neutralizing plasma antibodies effective against autologous circulating viruses in infants with multivariant HIV-1 infection
Some infants develop broadly neutralizing antibodies (bnAbs) to HIV in a shorter time frame than adults, but the reasons aren’t well understood. Here, the authors study a cohort of 51 HIV-1 clade C perinatally infected infants of Indian origin and find that multivariant infection is associated with bnAbs in elite neutralizers.
- Nitesh Mishra
- , Shaifali Sharma
- & Kalpana Luthra
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Article
| Open AccessChronic bee paralysis as a serious emerging threat to honey bees
Chronic bee paralysis is a viral disease of honey bees with a global distribution, but its epidemiology isn’t well understood. Here, Budge et al., using government honey bee health inspection records from England and Wales, demonstrate the disease is emergent and highlight periodic reintroduction of the disease between years.
- Giles E. Budge
- , Nicola K. Simcock
- & Steve P. Rushton
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Article
| Open AccessDisentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza
The role of Africa in the global spread of highly pathogenic avian influenza (HPAI) is not well understood. Here, using evolutionary analyses, the authors show that Africa mainly acts as ecological sink for HPAI H5, and reveal varying paths of HPAI incursions either through domestic or wild birds.
- Alice Fusaro
- , Bianca Zecchin
- & Isabella Monne
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Article
| Open AccessAedes mosquitoes acquire and transmit Zika virus by breeding in contaminated aquatic environments
Here the authors show that Aedes mosquitoes can acquire ZIKV by breeding in contaminated aquatic systems, and that these infected mosquitoes can transmit ZIKV to susceptible mice. This suggests that human urine containing aquatic environments could contribute to ZIKV transmission.
- Senyan Du
- , Yang Liu
- & Gong Cheng
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| Open AccessPredicting wildlife reservoirs and global vulnerability to zoonotic Flaviviruses
Flaviviruses have emerged or re-emerged in several regions, but factors underlying emergence are incompletely understood. Here, Pandit et al. identify potential sylvatic reservoirs of flaviviruses and, in combination with vector distribution data, predict regions of global vulnerability.
- Pranav S. Pandit
- , Megan M. Doyle
- & Christine K. Johnson
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Article
| Open AccessThe geography of measles vaccination in the African Great Lakes region
The WHO targets measles elimination by 2020, a goal that relies on high vaccination coverage. Here, Takahashiet al. identify ‘coldspots’ in the African Great Lakes region where measles vaccine coverage is below 80%, suggesting that these regions should be targeted in future vaccination campaigns.
- Saki Takahashi
- , C. Jessica E. Metcalf
- & Justin Lessler
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Article
| Open AccessEnvelope-specific B-cell populations in African green monkeys chronically infected with simian immunodeficiency virus
Infection of African green monkeys with simian immunodeficiency virus is a potential model for HIV vaccine development. Here, Zhang et al. catalogue the immunoglobulin loci present in the genome of these animals, and experimentally study their B-cell response to the viral envelope protein.
- Ruijun Zhang
- , David R. Martinez
- & Sallie R. Permar
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Article
| Open AccessVector-free transmission and persistence of Japanese encephalitis virus in pigs
Japanese encephalitis virus (JEV) is primarily transmitted between mosquitoes and birds but can also infect pigs. Here the authors demonstrate that JEV, which was thought to be spread exclusively by mosquitoes, can be transmitted between pigs through a direct contact.
- Meret E. Ricklin
- , Obdulio García-Nicolás
- & Artur Summerfield
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Article
| Open AccessRapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late 2014
Norovirus GII.4 has been predominating in viral gastroenteritis for 20 years. Here the authors report the emergence and predominance of a novel fast-evolving GII.17 lineage norovirus causing viral gastroenteritis in Hong Kong, with a shift in age distribution of affected individuals towards an older age as compared to GII.4.
- Martin C. W. Chan
- , Nelson Lee
- & Paul K. S. Chan
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Article
| Open AccessMammalian adaptation of influenza A(H7N9) virus is limited by a narrow genetic bottleneck
H7N9 bird flu viruses cause mild disease in poultry but can occasionally infect humans with fatal consequences. Here, the authors show that viral genetic diversification is low in ferrets and high in chickens, suggesting that a genetic bottleneck limits H7N9 adaptation to mammals
- Hassan Zaraket
- , Tatiana Baranovich
- & Richard J. Webby
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Structural basis for preferential avian receptor binding by the human-infecting H10N8 avian influenza virus
Avian strains of the influenza virus sometimes infect human hosts with severe consequences. Here, Wang et al.report that the H10N8 avian influenza virus, for which two lethal human infections have been reported, possesses restricted affinity towards the human receptor and suggest a structural basis for H10N8’s limited virulence.
- Min Wang
- , Wei Zhang
- & George F. Gao
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Using geospatial modelling to optimize the rollout of antiretroviral-based pre-exposure HIV interventions in Sub-Saharan Africa
Widespread use of antiretroviral drugs for HIV prevention is under evaluation in Sub-Saharan Africa. Here, Gerberry et al.use geospatial mathematical modelling to compare potential rollout plans and show that the initial resource allocation decisions will be crucial in determining the success of interventions.
- David J. Gerberry
- , Bradley G. Wagner
- & Sally Blower
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Article
| Open AccessEvidence for henipavirus spillover into human populations in Africa
Henipaviruses (HNVs) infect bats in Asia and Africa, but transmission to humans (often with lethal consequences) is known only in Asia. Here the authors show that 3% of human serum samples from certain areas in Cameroon contain antibodies against HNV, indicating spillover into the human population.
- Olivier Pernet
- , Bradley S. Schneider
- & Benhur Lee
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| Open AccessPredicting the risk of avian influenza A H7N9 infection in live-poultry markets across Asia
An avian influenza virus of the H7N9 type, associated with live-poultry markets, has caused two human epidemics in China. Here, the authors develop a statistical model that predicts the risk of H7N9 infection in live-poultry markets across Asia, as a tool for disease surveillance and control.
- Marius Gilbert
- , Nick Golding
- & Hongjie Yu
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Multi-peaked adaptive landscape for chikungunya virus evolution predicts continued fitness optimization in Aedes albopictus mosquitoes
The ability of a pathogen to adapt to new hosts affects its ability to spread in new environments. Here, Tsetsarkin et al.analysed mutations that enabled the chikungunya virus to adapt to a mosquito vector and predict that specific mutations will result in greater transmission efficiency.
- Konstantin A. Tsetsarkin
- , Rubing Chen
- & Scott C. Weaver
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Dynamic reassortments and genetic heterogeneity of the human-infecting influenza A (H7N9) virus
H7N9 influenza A viruses capable of infecting humans have recently emerged in China. Here, the authors show that these viruses remain genetically diverse, suggesting that they are still in the process of adapting to human hosts.
- Lunbiao Cui
- , Di Liu
- & George F. Gao
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Article
| Open AccessInterferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals
A variant in the IFITM3gene increases the risk of severe influenza, but homozygosity is rare in Caucasians. The authors show that the variant gene is homozygous in 25% of healthy Chinese people, and 69% of those with severe pandemic influenza, suggesting that this gene influences the epidemiology of influenza in South-East Asia.
- Yong-Hong Zhang
- , Yan Zhao
- & Tao Dong
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Article
| Open AccessSoil clay content underlies prion infection odds
The infectious prion diseases affect numerous hoofed animal species, and it has been suggested that the properties of the local soil affect transmission of these diseases. Here, the authors studied two North American locations and demonstrate that soil clay content can influence the infection rate in deer.
- W. David Walter
- , Daniel P. Walsh
- & Michael W. Miller