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Data

narrativeDataNarrative

Narrative 2 | Cross-border virus transmission

English: To gain insights into the the emergence, spread, and transmission of COVID-19 in our community, we are working with a large number of partners to sequence SARS-CoV-2 samples from patients in San Diego and across the border in Tijuana. In this preliminary analysis we look at the how the outbreaks are connected between California, USA and Baja California, (more…)
July 31, 2020
narrativeDataNarrative

Narrative 1 | Genomic Epi in San Diego

To gain insights into the the emergence, spread, and transmission of COVID-19 in our community, we are working with a large number of partners to sequence SARS-CoV-2 samples from infected patients in San Diego. This is our first preliminary analysis. (more…)
June 18, 2020
figure 3Data

Hidden Zika outbreak

Summary: Using local and travel-associated case reporting from American and European public health systems, we identified an unreported Zika outbreak in Cuba during 2017. Virus sequencing from travelers revealed that the Zika outbreak in Cuba was sparked by multiple introductions of the virus from elsewhere in the Caribbean and Central America during 2016 that persisted into 2017. The recent Zika virus…
July 3, 2018
figure 1DataNews

PAHO Zika numbers

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…
June 26, 2017
DataNews

Zika sequences from Miami mosquitoes

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. (more…)
September 10, 2016
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