DataNews

Zika sequence from local Florida transmission

Data here. Protocol here. In collaboration with Dr. Diogo Magnani in the Watkins Laboratory in the Dept. of Pathology at the University of Miami's Miller School of Medicine, we recently received plasma and saliva from two people with Zika virus infections living in the Miami area. Using our amplicon-based approach previously used to sequence Zika virus from travel-related Zika virus cases in…
September 7, 2016
DataProtocols

Travel-related Zika cases in Florida

Figure 1. Coverage plots of the included samples. Data here. Protocol here. In a collaboration with Scott Michael and Sharon Isern from Florida Gulf Coast University and Florida Department of Health, we have recently received several travel-related cases detected across Florida. We have now managed to sequence Zika virus genomes from three of these case and the data and analyses can be accessed here. (more…)
August 30, 2016
DataProtocols

MiSeq protocol for Zika virus sequencing

Amplicon-based protocol for Zika virus sequencing on the Illumina MiSeq The protocol can be found here. Figure 1. Sequencing coverage of the Zika virus genome. Zika virus strain PRVABC59 spiked with Hela RNA was PCR amplified using 70 virus-specific primers in two reactions, prepared for sequencing using the Kapa Hyper prep kit, and sequenced using the MiSeq v2 500 cycle…
August 26, 2016
ratesPublications

Flawed Ebola study in Science

In a technical comment in Science, we show how a study published in 2015 by Hoenen, Feldmann, and others was based on faulty analyzes and a misunderstanding of the findings. The original article by the authors, as well as a later published erratum, failed to account for significant data analysis errors performed by Hoenen and colleagues.  (more…)
August 12, 2016
NewsPublications

Navigating the Zika panic

The epidemics of Ebola virus in West Africa and Zika virus in America highlight how viruses can explosively emerge into new territories. These epidemics also exposed how unprepared we are to handle infectious disease emergencies. This is also true when we consider hypothesized new clinical features of infection, such as the associations between Zika virus infection and severe neurological disease,…
August 4, 2016
Data

Zika virus pilot (update)

We have now received several hundred de-identified clinical samples from the Dominican Republic and Colombia. Unfortunately, they all have extremely low viral lows (Ct values > 38 in the few that are positive), so we’re continuing our technology development. We are following a couple of different strategies: (more…)
July 21, 2016
Publications

Roots, Not Parachutes

Infectious disease outbreaks continue to pose challenges to global health and security, prompting reactive countermeasures. Recently, severe outbreaks of Ebola and Zika virus were designated by the World Health Organization as “Public Health Emergencies of International Concern.” Other emerging viral pathogens have warranted similar attention, including virus outbreaks from Lassa, Chikungunya, avian influenza, Nipah, SARS, and MERS. (more…)
June 30, 2016
Data

Zika virus pilot

We recently received plasma samples from Zika virus (ZIKV) patients in Colombia. We performed QC on the samples and unfortunately very few had detectable levels of ZIKV by qPCR. We extracted RNA from two of these patient samples (Z184 and Z186), as well as a positive control (seed stock of the Malaysian strain P6-740 passaged once on BHK-21 cells) kindly…
April 5, 2016