data Archives | Andersen Lab


Age distribution of COVID-19 cases in San Diego County

To understand the spread of COVID-19 in San Diego, we looked at the age distribution of COVID-19 over time (Figure 1). Data for this analysis was provided by the Epidemiology and Immunization Services Branch of the County of San Diego Health and Human Services agency through the San Diego Open GIS Data Portal. The visualization was inspired by Gytis Dudas's…
November 24, 2020
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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
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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

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

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

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

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

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