色情视频

A multi-disciplinary team of experts in virology and computer modeling has quickly assembled at 色情视频 to learn more about how the new coronavirus (COVID-19) spreads in the environment and how its trajectory can be better predicted.

It is well-known that COVID-19 does not survive on surfaces that are frequently cleaned and sanitized, but what about surfaces in high traffic areas that are not routinely cleaned, such as gas station pumps, park benches and ATMs?  

Recognizing the urgency and need for this research, the National Science Foundation has awarded 色情视频鈥檚 viral ecologist Forest Rohwer and his 色情视频 collaborator, Naveen Vaidya, a mathematician with simulation modeling expertise, a  of $200,000. That is the maximum amount awarded under this program, and is designated to fast-track COVID-19 research.

The exploratory research Rohwer is leading serves two goals: It would help inform the California Department of Public Health and other public agencies about how the virus is spreading, and it could enable Rohwer鈥檚 team to determine if there are environmental reservoirs where the virus thrives, which is now a big question.

鈥淚f there are reservoirs in the city that are unknown, we have to be careful,鈥� Rohwer said. 鈥淚f we say the pandemic is over, and there are reservoirs we don鈥檛 know about, there could be outbreaks in the future. How do you rule that out? We have to do the best we can with our sampling.鈥�

Public can help with sampling

A couple of weeks before the world woke up to the seriousness of COVID-19, virologists across the country met at 鈥淭he Global Virome in Health and Disease鈥� Keystone Symposia in Lake Tahoe, California where Rohwer delivered the keynote address on phage therapy.

One common belief prevailed during the meeting: We were simply not prepared for the global pandemic.

Even before he returned home, Rohwer, who previously discovered how to sequence the somewhat similar SARS virus, placed orders for the reagents needed to study the coronavirus鈥� DNA. Reagents are compounds required to enable polymerase chain reaction (PCR) assay testing, when biologists make millions of copies of a specific DNA sample rapidly, so they can extract and study short strands of that DNA in more detail.

Back in the lab, Rohwer and his Ph.D. students began setting up the assays.

Their goal: While clinical researchers test and study the virus in humans, Rohwer and his students would leverage their expertise as environmental experts to study how the novel coronavirus was spreading in the community.

Since March, Rohwer鈥檚 doctoral students, Mark Little and Jason Baer, have been preparing test kits and collecting environmental samples using simple swabs in common public areas. To extend the areas of sampling, Rohwer鈥檚 team has now opened it up to the public.

Anyone interested in citizen science  and, depending on where they live in San Diego County,  may be selected to receive a test kit. The researchers are seeking about 1,000 people in different parts of the County to conduct sampling.

Each kit contains 20 vials filled with the reagent and a mild detergent that will inactivate the virus but stabilize and preserve its genetic material, and 20 swabs, as well as disposable gloves and two types of masks (N95, and the Montana Mask which is a 3D printable, reusable plastic mask), and instructions on how to proceed.

To help with tracking, citizen scientists will be asked to upload information about where they conducted the sampling, the GPS coordinates and photos of the sampling surface. The kits will be picked up when sampling is completed. Rohwer鈥檚 team is keeping the timeline open ended to ensure volunteers don鈥檛 rush the process or limit themselves to one area.

Extraction and analysis

Once the samples arrive in the lab, they鈥檙e stored in an -80 degree Celsius freezer. To maintain social distancing while conducting research, lab members work at different times of the day and only meet virtually.

Maria-Isabel Rojas, a microbiologist and Ph.D. candidate in Rohwer鈥檚 lab who leads the sample testing, spends long days in two different labs.   First, she takes the samples to a Biosafety Level 2 lab to isolate and extract the RNA, which she then converts into DNA via reverse transcription, so it can be amplified through the polymerase chain reaction (PCR) process.

Once she enters the lab where she conducts PCR assays, she can鈥檛 go back to the other lab on the same day, wearing the same clothes, as a precaution to prevent contamination of the samples.

鈥淲e work with such tiny amounts of the virus, so we are particularly careful about background contamination,鈥� Rojas said. 鈥淚 make sure to extract RNA from enough samples to get a full day鈥檚 worth of work in the PCR lab.鈥�

She is looking for a very specific DNA fragment of the coronavirus, using the PCR process.  

鈥淧icture the DNA as a length of rope made with building blocks: each block is a letter, and the blocks are organized in a certain order dictated by the genetic code,鈥� Rojas said.

To identify SARS-CoV-2, the U.S. Centers for Disease Control and Prevention has found a very specific combination of these building blocks present at certain points of the DNA strand.

鈥淭he sequencing of RNA and DNA will tell us if the coronavirus has stayed the same, or if it has mutated,鈥� Rojas said. 鈥淚f it has, we hope to be able to see how the virus is mutating, possibly so it can adapt better and last in the environment in certain reservoirs.鈥�

Building models to predict risk and trends

The data she gathers will then be fed into models that will predict the risk of transmission from the environment, and what the trajectory of this disease would look like.

To do this, Rohwer will loop in mathematical and computational modeling expert Vaidya, who has expertise in building simulation models for various infectious diseases including the flu virus, to predict trends for how the SARS-CoV-2 virus behaves as it spreads.

鈥淲ith a few weeks鈥� worth of data we can estimate the risk of infection from the environmental virus and try to mimic what鈥檚 happening with simulation models that predict transmission trends,鈥� Vaidya said. 鈥淭his will also help us see how to ramp up cleaning surfaces, for example.鈥�

Vaidya is also using transmission parameters from the outbreaks in Wuhan, China, Italy and elsewhere, and will adapt it for San Diego County鈥檚 population.

These include parameters such as the latent period when people are infected, but not yet infectious. The predictions from his modeling will help inform public health officials on where to focus their efforts next.

As this research evolves, Rohwer will also bring in additional 色情视频 researchers, computational biologist Rob Edwards and marine microbiologist Elizabeth Dinsdale, to harness their expertise in further analyzing the virus.   

The researchers involved in this COVID-19 study are part of 色情视频鈥檚 , a cross-disciplinary coalition of scientists鈥攄rawn from biology, math, computer science, chemistry and physics鈥攅xploring viruses from different angles. This research has also received donor funding from 色情视频 alumna and faculty emerita Jo Ann Lane.

鈥淚n addition to improving our current knowledge of SARS-CoV-19, this research will be important for the continuing response to CoVID-19 and future pandemics,鈥� Rohwer said.

鈥淭his study will help us understand the ecology of viral-human interactions on surfaces, as well as train the next-generation of field virologists and modelers.鈥�