Data here. Permanent Andersen Lab project link is 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…
In a series of papers in the journals Nature and Nature Protocols, we used Zika virus sequencing from patients and mosquitos to show how the virus has spread across South America and into Florida. This work was performed as a large (huge!) collaboration of national and international institutions, which was made possible because of open science and open data.
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.
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…
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.
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.
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:
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.