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Data

PAHO Zika numbers

By | Data, News

Data here. Permanent Andersen Lab project link here. Most epidemiological investigations of Zika virus during the current epidemic in the Americas requires temporal human case data. The only place to gather this information is is from the Pan American Health Organization (PAHO), an arm of the World Health Organization. They present Zika virus case numbers in two ways: spreadsheets of cumulative case…

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Zika sequences from Miami mosquitoes

By | Data, News

Data here. Protocol here. Three pools of Aedes aegypti mosquitoes collected in Miami Beach on August 22nd and 23rd, 2016, were found to be infected with Zika virus. Through our collaborators, Scott Michael and Sharon Isern from Florida Gulf Coast University, we recently received samples of these mosquitoes for sequencing using our amplicon-based protocol for MiSeq.

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Zika sequence from local Florida transmission

By | Data, News

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…

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Travel-related Zika cases in Florida

By | Data, Protocols

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.

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MiSeq protocol for Zika virus sequencing

By | Data, Protocols

Amplicon-based protocol for Zika virus sequencing on the Illumina MiSeq The protocol can be found here. Sequencing Zika virus from the ongoing epidemic in the Americas is of critical importance. Data from the viral genome will help us determine how the virus is spreading, changes to viral population sizes, and if the virus is adapting to local conditions.

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Zika virus pilot (update)

By | Data

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:

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Zika virus pilot

By | Data | No Comments

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…

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