M. Kate Grabowski

Bio: M. Kate Grabowski is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Population & Viral load. The author has an hindex of 14, co-authored 32 publications receiving 565 citations. Previous affiliations of M. Kate Grabowski include University of KwaZulu-Natal & Johns Hopkins University School of Medicine.

Household COVID-19 risk and in-person schooling

Abstract: In-person schooling has proved contentious and difficult to study throughout the SARS-CoV-2 pandemic. Data from a massive online survey in the United States indicates an increased risk of COVID-19-related outcomes among respondents living with a child attending school in-person. School-based mitigation measures are associated with significant reductions in risk, particularly daily symptoms screens, teacher masking, and closure of extra-curricular activities. A positive association between in-person schooling and COVID-19 outcomes persists at low levels of mitigation, but when seven or more mitigation measures are reported, a significant relationship is no longer observed. Among teachers, working outside the home was associated with an increase in COVID-19-related outcomes, but this association is similar to other occupations (e.g., healthcare, office work). While in-person schooling is associated with household COVID-19 risk, this risk can likely be controlled with properly implemented school-based mitigation measures.

HIV Prevention Efforts and Incidence of HIV in Uganda

Abstract: BackgroundTo assess the effect of a combination strategy for prevention of human immunodeficiency virus (HIV) on the incidence of HIV infection, we analyzed the association between the incidence of HIV and the scale-up of antiretroviral therapy (ART) and medical male circumcision in Rakai, Uganda. Changes in population-level viral-load suppression and sexual behaviors were also examined. MethodsBetween 1999 and 2016, data were collected from 30 communities with the use of 12 surveys in the Rakai Community Cohort Study, an open, population-based cohort of persons 15 to 49 years of age. We assessed trends in the incidence of HIV on the basis of observed seroconversion data, participant-reported use of ART, participant-reported male circumcision, viral-load suppression, and sexual behaviors. ResultsIn total, 33,937 study participants contributed 103,011 person-visits. A total of 17,870 persons who were initially HIV-negative were followed for 94,427 person-years; among these persons, 931 seroconversions were...

The engines of SARS-CoV-2 spread.

Abstract: Fighting SARS-CoV-2 requires a clear framework for understanding epidemic spread Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly across the globe, causing epidemics that range from quickly controlled local outbreaks (such as New Zealand) to large ongoing epidemics infecting millions (such as the United States). A tremendous volume of scientific literature has followed, as has vigorous debate about poorly understood facets of the disease, including the relative importance of various routes of transmission, the roles of asymptomatic and presymptomatic infections, and the susceptibility and transmissibility of specific age groups. This discussion may create the impression that our understanding of transmission is frequently overturned. Although our knowledge of SARS-CoV-2 transmission is constantly deepening in important ways, the fundamental engines that drive the pandemic are well established and provide a framework for interpreting this new information.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

Abstract: Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.

Open data sharing and the Global South—Who benefits?

Abstract: A growing number of government agencies, funding organizations, and publishers are endorsing the call for increased data sharing, especially in biomedical research, many with an ultimate goal of open data Open data is among the least restrictive forms of data sharing, in contrast to managed access mechanisms, which typically have terms of use and in some cases oversight by the data generators themselves But despite an ethically sound rationale and growing support for open data sharing in many parts of the world, concerns remain, particularly among researchers in low- and middle-income countries (LMICs) in Africa, Latin America, and parts of Asia and the Middle East that comprise the Global South Drawing on our perspective as researchers and ethicists working in the Global South, we see opportunities to improve community engagement, raise awareness, and build capacity, all toward improving research and data sharing involving researchers in LMICs

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Airborne transmission of respiratory viruses.

Abstract: The COVID-19 pandemic has revealed critical knowledge gaps in our understanding of and a need to update the traditional view of transmission pathways for respiratory viruses. The long-standing definitions of droplet and airborne transmission do not account for the mechanisms by which virus-laden respiratory droplets and aerosols travel through the air and lead to infection. In this Review, we discuss current evidence regarding the transmission of respiratory viruses by aerosols-how they are generated, transported, and deposited, as well as the factors affecting the relative contributions of droplet-spray deposition versus aerosol inhalation as modes of transmission. Improved understanding of aerosol transmission brought about by studies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requires a reevaluation of the major transmission pathways for other respiratory viruses, which will allow better-informed controls to reduce airborne transmission.