Integrating Phylogenetic Biomarker Data and Qualitative Approaches: An example of HIV Transmission Clusters as a Sampling Frame for Semistructured Interviews and Implications for the COVID-19 Era.

Mixed methods studies of human disease that combine surveillance, biomarker, and qualitative data can help elucidate what drives epidemiological trends. Viral genetic data are rarely coupled with other types of data due to legal and ethical concerns about patient privacy. We developed a novel approach to integrate phylogenetic and qualitative methods in order to better target HIV prevention efforts.

Geospatial Analysis of COVID-19: A Scoping Review.

The outbreak of SARS-CoV-2 in Wuhan, China in late December 2019 became the harbinger of the COVID-19 pandemic. During the pandemic, geospatial techniques, such as modeling and mapping, have helped in disease pattern detection. Here we provide a synthesis of the techniques and associated findings in relation to COVID-19 and its geographic, environmental, and socio-demographic characteristics, following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) methodology for scoping reviews.

Non-B variants of HIV-1 in San Francisco, California.

The HIV-1 epidemic in the US has historically been dominated by subtype B. HIV subtype diversity has not been extensively examined in most US cities to determine whether non-B variants have become established, as has been observed in many other global regions. We describe the diversity of non-B variants and present evidence of local transmission of non-B HIV in San Francisco.

How are transgender women acquiring HIV? Insights from phylogenetic transmission clusters in San Francisco.

Objective: We explored potential HIV transmission typologies that involve transgender women to obtain insights on sexual and needle-sharing networks as sources of HIV infection.

Design: San Francisco residents diagnosed with HIV in care at public facilities who had available viral pol sequences from June 2001 to January 2016 were included in the analysis.

Methods: Viral sequence data were matched to the San Francisco HIV/AIDS Case Registry to obtain demographic and risk classification information.

Increased uptake of early initiation of antiretroviral therapy and baseline drug resistance testing in San Francisco between 2001 and 2015.

Background: Early initiation of antiretroviral therapy (eiART) can improve clinical outcomes for persons with HIV and reduce onward transmission risk. Baseline drug resistance testing (bDRT) can inform regimen selection upon subsequent treatment initiation. We examined the uptake of eiART and bDRT within 3 months and 30 days of HIV diagnosis.

Frequent coinfection reduces RNA virus population genetic diversity.

The masking of deleterious mutations by complementation and the reassortment of virus segments (virus sex) are expected to increase population genetic diversity among coinfecting viruses. Conversely, clonally reproducing or noncoinfecting virus populations may experience clonal interference where viral clones compete with one another, preventing selective sweeps. This dynamic reduces the efficiency of selection and increases the genetic diversity.

People fifty years or older now account for the majority of AIDS cases in San Francisco, California, 2010.

People aged 50 and older are an increasing proportion of the population of persons living with AIDS (PLWA) in the USA. We used San Francisco's population-based HIV/AIDS surveillance registry to examine trends in the age distribution of people diagnosed and living with AIDS in San Francisco, California. AIDS case reporting is highly complete.

Geographic differences in sexual reassortment in RNA phage.

The genetic structure of natural bacteriophage populations is poorly understood. Recent metagenomic studies suggest that phage biogeography is characterized by frequent migration. Using virus samples mostly isolated in Southern California, we recently showed that very little population structure exists in segmented RNA phage of the Cystoviridae family due to frequent segment reassortment (sexual genetic mixis) between unrelated virus individuals.

Playing by different rules: the evolution of virulence in sterilizing pathogens.

We investigate the evolution of virulence of pathogens that reduce their hosts' fitness primarily by affecting host fecundity. We show that, under many conditions, such sterilizing pathogens evolve high rather than intermediate levels of virulence, and this pushes the pathogen population and sometimes the host population toward extinction. We also show that spatial population structure can reverse this evolutionary result and allow the persistence of intermediate-virulence pathogens.

Widespread genetic exchange among terrestrial bacteriophages.

Bacteriophages are the most numerous entities in the biosphere. Despite this numerical dominance, the genetic structure of bacteriophage populations is poorly understood. Here, we present a biogeography study involving 25 previously undescribed bacteriophages from the Cystoviridae clade, a group characterized by a dsRNA genome divided into three segments.

The evolution of virulence in pathogens with frequency-dependent transmission.

Frequency-dependent transmission is an important feature of diseases that are sexually transmitted or transmitted by a vector that actively searches for hosts. Here I describe the evolution of virulence in pathogens that have frequency-dependent transmission. I consider two components of virulence--an increase in host mortality due to infection, as is classically described, and a decrease in host fecundity due to infection, because frequency dependence is common among diseases that fully or partially sterilize their hosts.