11 Result(s)
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Karthik Gangavarapu
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Article
Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources
Outbreak.info Research Library is a standardized, searchable interface of coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) publications, clinical trials, dat...
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Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. T...
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Open AccessPredicting the evolution of the Lassa virus endemic area and population at risk over the next decades
Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could aff...
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Open AccessWastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially ...
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Open AccessRegional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions
Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connect...
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Open AccessEpidemiological hypothesis testing using a phylogeographic and phylodynamic framework
Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spati...
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Open AccessAn amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentra...
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Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Genome sequencing of Zika virus samples from infected patients and Aedes aegypti mosquitoes in Florida shows that the virus was probably introduced into the United States on multiple occasions, and that the Carib...
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Zika virus evolution and spread in the Americas
One hundred and ten Zika virus genomes from ten countries and territories involved in the Zika virus epidemic reveal rapid expansion of the epidemic within Brazil and multiple introductions to other regions.
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Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
This multiplex PCR enrichment protocol enables sequencing of Zika and other viral genomes of low abundance from clinical samples using the Illumina platform, or the portable MinION sequencer, facilitating dire...
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Open AccessCIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and predisposing relevance of inherited and somatic variants o...
