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View article: Cross-protective HCoV immunity reduces symptom development during SARS-CoV-2 infection
Cross-protective HCoV immunity reduces symptom development during SARS-CoV-2 infection Open
Knowledge of the interplay between human coronavirus (HCoV) immunity and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection is critical to understanding the coexistence of current endemic coronaviruses and to build…
View article: Incidence of sexually transmitted infections and association with behavioural factors: Time‐to‐event analysis of a large pre‐exposure prophylaxis (<scp>PrEP</scp>) cohort
Incidence of sexually transmitted infections and association with behavioural factors: Time‐to‐event analysis of a large pre‐exposure prophylaxis (<span>PrEP</span>) cohort Open
Objectives Our objective was to obtain long‐term data on the incidence of sexually transmitted infections (STIs) and their association with behavioural factors after widespread pre‐exposure prophylaxis (PrEP) implementation. Methods This w…
View article: Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018
Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018 Open
Background Genotypic resistance testing (GRT) is routinely performed upon diagnosis of HIV-1 infection or during virological failure using plasma viral RNA. An alternative source for GRT could be cellular HIV-1 DNA. Objectives A substantia…
View article: A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits
A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits Open
Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent ob…
View article: Antibodies from convalescent plasma promote SARS-CoV-2 clearance in individuals with and without endogenous antibody response
Antibodies from convalescent plasma promote SARS-CoV-2 clearance in individuals with and without endogenous antibody response Open
BACKGROUNDNeutralizing antibodies are considered a key correlate of protection by current SARS-CoV-2 vaccines. The manner in which human infections respond to therapeutic SARS-CoV-2 antibodies, including convalescent plasma therapy, remain…
View article: Antibodies from convalescent plasma promote SARS-CoV-2 clearance in individuals with and without endogenous antibody response
Antibodies from convalescent plasma promote SARS-CoV-2 clearance in individuals with and without endogenous antibody response Open
BACKGROUND. Neutralizing antibodies are considered a key correlate of protection by current SARS-CoV-2 vaccines. The manner in which human infections respond to therapeutic SARS-CoV-2 antibodies, including convalescent plasma therapy, rema…
View article: A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study
A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study Open
Background Studying human immunodeficiency virus type 1 (HIV-1) superinfection is important to understand virus transmission, disease progression, and vaccine design. But detection remains challenging, with low sampling frequencies and ins…
View article: Sustained Effect on Hepatitis C Elimination Among Men Who Have Sex With Men in the Swiss HIV Cohort Study: A Systematic Re-Screening for Hepatitis C RNA Two Years Following a Nation-Wide Elimination Program
Sustained Effect on Hepatitis C Elimination Among Men Who Have Sex With Men in the Swiss HIV Cohort Study: A Systematic Re-Screening for Hepatitis C RNA Two Years Following a Nation-Wide Elimination Program Open
Background The Swiss HCVree Trial (NCT 02785666) was conducted in 2015–2017 with the goal of implementing a population-based systematic hepatitis C virus (HCV) micro-elimination program among men who have sex with men (MSM) with human immu…
View article: An Approach to Quantifying the Interaction between Behavioral and Transmission Clusters
An Approach to Quantifying the Interaction between Behavioral and Transmission Clusters Open
We hypothesize that patterns of sexual behavior play a role in the conformation of transmission networks, i.e., the way you behave might influence whom you have sex with. If that was the case, behavioral grouping might in turn correlate wi…
View article: Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics
Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics Open
Objectives: Phylogenetic analyses of 2 or more countries allow to detect differences in transmission dynamics of local HIV-1 epidemics beyond differences in demographic characteristics. Methods: A maximum-likelihood phylogenetic tree was b…
View article: ICE volume 43 issue 3 Cover and Front matter
ICE volume 43 issue 3 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: Detecting Selection in the HIV-1 Genome during Sexual Transmission Events
Detecting Selection in the HIV-1 Genome during Sexual Transmission Events Open
Little is known about whether and how variation in the HIV-1 genome affects its transmissibility. Assessing which genomic features of HIV-1 are under positive or negative selection during transmission is challenging, because very few virus…
View article: A highly virulent variant of HIV-1 circulating in the Netherlands
A highly virulent variant of HIV-1 circulating in the Netherlands Open
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log 10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhi…
View article: Prevalence of Occult Hepatitis B Virus Infection in Blood Donors with Negative ID-NAT in Switzerland
Prevalence of Occult Hepatitis B Virus Infection in Blood Donors with Negative ID-NAT in Switzerland Open
Introduction: Screening of hepatitis B surface antigen (HBsAg) and individual-donation nucleic acid amplification testing (ID-NAT) of blood donors have become standard to detect hepatitis B virus (HBV) infection. However, there is still a …
View article: Contribution of endogenous and exogenous antibodies to clearance of SARS-CoV-2 during convalescent plasma therapy
Contribution of endogenous and exogenous antibodies to clearance of SARS-CoV-2 during convalescent plasma therapy Open
Neutralizing antibodies are considered a key correlate of protection by current SARS-CoV-2 vaccines. The ability of antibody-based therapies, including convalescent plasma, to affect established disease remains to be elucidated. Only few m…
View article: A phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits
A phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits Open
Infectious diseases are a unique challenge for genome-wide association studies (GWAS) because pathogen, host, and environmental factors can all affect disease traits. Previous GWAS have successfully identified several human genetic variant…
View article: Multifactorial seroprofiling dissects the contribution of pre-existing human coronaviruses responses to SARS-CoV-2 immunity
Multifactorial seroprofiling dissects the contribution of pre-existing human coronaviruses responses to SARS-CoV-2 immunity Open
Determination of SARS-CoV-2 antibody responses in the context of pre-existing immunity to circulating human coronavirus (HCoV) is critical for understanding protective immunity. Here we perform a multifactorial analysis of SARS-CoV-2 and H…
View article: Decreasing Incidence and Determinants of Bacterial Pneumonia in People With HIV: The Swiss HIV Cohort Study
Decreasing Incidence and Determinants of Bacterial Pneumonia in People With HIV: The Swiss HIV Cohort Study Open
Background Bacterial pneumonia is a leading reason for hospitalization among people with HIV (PWH); however, evidence regarding its drivers in the era of potent antiretroviral therapy is limited. Methods We assessed risk factors for bacter…
View article: Management of Suspected Cases of Feline Immunodeficiency Virus Infection in Eurasian Lynx (Lynx lynx) During an International Translocation Program
Management of Suspected Cases of Feline Immunodeficiency Virus Infection in Eurasian Lynx (Lynx lynx) During an International Translocation Program Open
The Eurasian lynx ( Lynx lynx ) population in Switzerland serves as a source for reintroductions in neighboring countries. In 2016–2017, three lynx from the same geographical area were found seropositive for feline immunodeficiency virus (…
View article: Participation, retention and uptake in a multicentre pre‐exposure prophylaxis cohort using online, smartphone‐compatible data collection
Participation, retention and uptake in a multicentre pre‐exposure prophylaxis cohort using online, smartphone‐compatible data collection Open
Objectives The aim of the study was to assess the feasibility of a national pre‐exposure prophylaxis (PrEP) programme using smartphone‐compatible data collection. Methods This was a multicentre cohort study (NCT03893188) enrolling individu…
View article: An approach to quantifying the interaction between behavioural and transmission clusters: the case of Hepatitis C virus infections in HIV positive men who have sex with men
An approach to quantifying the interaction between behavioural and transmission clusters: the case of Hepatitis C virus infections in HIV positive men who have sex with men Open
We hypothesize that patterns of sexual behaviour play a role in the conformation of transmission networks. If that was the case, behavioural grouping might in turn correlate with transmission networks and have the potential to predict prox…
View article: Reduced Relative Sensitivity of the Elecsys SARS-CoV-2 Antigen Assay in Saliva Compared to Nasopharyngeal Swabs
Reduced Relative Sensitivity of the Elecsys SARS-CoV-2 Antigen Assay in Saliva Compared to Nasopharyngeal Swabs Open
Early identification and isolation of SARS-CoV-2-infected individuals is central to contain the COVID-19 pandemic. Nasopharyngeal swabs (NPS) serve as a specimen for detection by RT-PCR and rapid antigen screening tests. Saliva has been co…
View article: Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link
Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link Open
Background: Considering the remaining threat of drug-resistantmutations (DRMs) to antiretroviral treatment (ART) efficacy, we investigated how the selective pressure of human leukocyte antigen (HLA)-restricted cytotoxic T lymphocytes drive…
View article: Author response: Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link
Author response: Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link Open
Article Figures and data Abstract Introduction Materials and methods Results Discussion Data availability References Decision letter Author response Article and author information Metrics Abstract Background: Considering the remaining thre…
View article: Usefulness of the GenMark ePlex RPP assay for the detection of respiratory viruses compared to the FTD21 multiplex RT-PCR
Usefulness of the GenMark ePlex RPP assay for the detection of respiratory viruses compared to the FTD21 multiplex RT-PCR Open
Cartridge-based multiplex panels covering numerous pathogens offer an advantage of minimal hands-on-time and short time to result to commercial RT-PCR assays. In this study, we evaluated the performance of the ePlex respiratory pathogen pa…
View article: Secondary attack rates from asymptomatic and symptomatic influenza virus shedders in hospitals: Results from the TransFLUas influenza transmission study
Secondary attack rates from asymptomatic and symptomatic influenza virus shedders in hospitals: Results from the TransFLUas influenza transmission study Open
Objective: Nosocomial transmission of influenza is a major concern for infection control. We aimed to dissect transmission dynamics of influenza, including asymptomatic transmission events, in acute care. Design: Prospective surveillance s…
View article: Multifactorial seroprofiling dissects the contribution of pre-existing human coronaviruses responses to SARS-CoV-2 immunity
Multifactorial seroprofiling dissects the contribution of pre-existing human coronaviruses responses to SARS-CoV-2 immunity Open
Determination of SARS-CoV-2 antibody responses in the context of pre-existing immunity to circulating human coronavirus (HCoV) is critical to understanding protective immunity. Here we perform a multifactorial analysis of SARS-CoV-2 and HC…