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Sequencing

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
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
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
News

Feature in Politiken

The leading Danish newspaper Politiken had a feature on our work in the September 20th 2015 Sunday section. The article discusses our past and ongoing work with Lassa and Ebola. The full feature describes how we have investigated both Lassa and Ebola virus evolution based on our most recent papers in Cell and Science. (more…)
September 20, 2015
Publications

Lassa paper on the front page of Cell

In a large multi-disciplinary collaboration between partners in Sierra Leone, Nigeria, USA, and Europe, we have published our first study on Lassa virus evolution. The paper - which appears on the front page of the August issue of Cell - is the result of seven years of work on Lassa fever across West Africa. (more…)
August 13, 2015
Publications

Ebola paper out in Cell

In a large collaboration between the Viral Hemorrhagic Fever Consortium, Kenema Government Hospital, Harvard University, Broad Institute, Tulane University, Edinburgh University, the CDC, USAMRIID, and others we have just published a paper in Cell detailing the epidemiology, transmission, and evolution of Ebola virus over seven months in Sierra Leone.  (more…)
June 18, 2015
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