SARS-CoV-2 and viral diversity on inert surfaces in Ecuadorian cities

Detection of SARS-CoV-2 and analysis of viral diversity on inert surfaces in urban spaces of three major Ecuadorian cities.

Juan José Guadulpe, M.Sc.

Auxiliary Profesor - Universidad San Francisco de Quito

Investigator - Plant Biotechnology Laboratory USFQ

The Principal Investigator of the Laboratory is María de Lourdes Torres, Ph.D.

• Identify: Genomic data to predict emerging risk is the specific problem within the challenge that we are trying to solve.  
• There is a lack of information regarding the presence of SARS-CoV-2 on inert surfaces in urban spaces. There are very few studies worldwide that address this topic. To fully understand the behavior of the virus we are dealing with, this data is also relevant. 
• Understanding the microbiome of environmental spaces including urban spaces is important, ... para que? however, this is also an area where there is a lack of information.  If we want to be better prepared for the next pandemic(s), we should be aware of the viruses that can be found in the environments we live in such as cities. de que manera? tener esta información nos ayuda a conocer los virus con los que convivimos y esto puede tener repercuciones en las estrategias en salud publica y estar mejor preparados para nuevas pandemias
• One reason for this knowledge gap, especially in a country like Ecuador, is that genomic characterization of environmental viral and microbial communities has not been a priority in our country. This pandemic has opened our eyes that genomic surveillance, microbial and viral communities characterization, surfaces viral prevalence could be useful information for developing appropriate public health policies that allow us to prevent and manage pandemics. 

• The data we obtain will be helpful to public health authorities at the national and local levels, such as the Ecuadorian Ministry of Public Health, and the municipalities of the cities where our study will be conducted. The results of this solution could aid the management and mobility strategies during the covid pandemic. Furthermore, the knowledge of urban space viromes can help put in place prevention mechanisms for future pandemics. 
• Epidemiologists and other researchers can use our data and build on it for their own investigations. Our standardized environmental SARS-CoV-2 LAMP mediated detection protocol will also be helpful for others who wish to analyze SARS-CoV-2 presence. Additionally, the protocol can be adapted for detection of other pathogens. 
• In order to assist public health authorities and other researchers, we will publish our data and protocols in reports and peer-reviewed journals. We also plan on conducting workshops in order to present our findings and teach other scientists how to use implement our methodology. We will also make our data accessible on open-source databases. 

The Ecuadorian government has failed in terms of testing, genomic surveillance, and research support in this pandemic. The present project will try to provide information that could aid in decision-making for crisis management and prevention strategies.

Moreover, the information we will provide will allow the general population to understand the relevance of viral prevalence on inert surfaces in cities. Press releases of our findings will also be relevant since the general population needs to be informed in times of crisis. 

For this study, samples will be collected in a non-discriminatory unbiased manner trying to cover diverse urban spaces within representative areas in the studied cities. 

Data from the study will be used for peer-review publications and uploaded to open source databases for further studies by other groups and scientists. Furthermore, the methodologies used in the present project can be used for related studies in pathogen detection and surveillance.

We expect that our results will give the general population an idea about SARS-CoV-2 presence on surfaces and the environment they live in, as well as a characterization of other viruses among us. Even though the main way of SARS-CoV-2 transmission is close contact person-to-person through small aerosol respiratory droplets, it is important to know where this virus is present and how it is circulating. General disinfection guidelines have shown to be effective against viral particles in surfaces, however, we believe it is important to show real data that in turn will make people realize how exposed they actually are. This information will highlight the importance of permanently adopting certain behaviours such as frequent hand washing and surface disinfection.

We believe that knowledge is power and that our research could help decision-makers, governmental agencies, and the general public establish prevention and management strategies. 

Moreover, the methodologies used in this study could be used for future studies referring to viruses and urban spaces.

The present study will work as a baseline for future projects. Information gathered from this study will help us understand the diversity that surrounds us and its importance in our daily lives. Fifty-four percent of human populations live in cities nowadays and interactions with microbes and virus among us is relevant to public health (Afshinnekoo et al., 2015). Moreover, in Ecuador according to the last census, 62.7% of the population lived in cities (INEC,2010). Therefore, it is relevant for the population to know who are they cohabitating with. Methodology and data from the first year of this project will let us scale it up to include other urban spaces in Ecuador and have a more complete picture of what is happening in the country's cities, it will also work as a baseline for years to come. Temporary surveillance of the metagenomic composition of cities could be established as means of information and prevention in the next years. 

Works cited

Please view supplementary file.

• As a success measure, we will set up yearly reports about our findings, not just for publication through peer review, but also for decision-makers. We believe that the paths governmental agencies take according to our findings will be a way of understanding the impacts of our research
• Moreover, scientific communication will be an important factor in this project, press releases and symposiums will let us show our findings and moreover transmit the information in a responsible way avoiding misinterpretation. It is important to show the general population the viral composition they live with but it is more important to teach them why this is relevant why would they care and what impacts could they have in their daily lives
• Measuring the impact of this present public on the general population can be assessed by interviews and through the outcomes, our results can have in public health politics

Financing scientific research has never been a priority for the Ecuadorian government. Funding was already an important barrier in our country before, however it has become a bigger problem during the COVID-19 pandemic. Most of the scientific research done during the pandemic has been funded by private institutions. Finding external funding support such as the Trinity Challenge has become the only option for Ecuadorian scientists.

Technological limitations have also been a barrier in the country and thus, one of our main objectives is to implement cutting-edge technologies such as sequencing. Moreover, we believe that the implementation of technologies and methodologies as the ones present in this solution could open barriers for scientific research in Ecuador.

Molecular Biology reagents are imported into the country and are subject to taxation. Ecuadorian law is supposed to release taxes for university research, but the highly bureaucratic and complicated procedures make it a difficult and long process.  The University (USFQ) has been doing research in Ecuador for over 30 years and has overcome problems with reagent acquisition. Even though reagents are more expensive and take time to arrive, these are barriers we have already overcome. 

Affiliations of different members include:

• Plant Biotechnology Laboratory-USFQ (Quito-Ecuador)
• Microbiology Institute-USFQ 
• Galapagos Science Center
• University of North Carolina at Chapel Hill 
• Department of Biology, San Diego State University 
• Viral Information Institute, San Diego State University 

Additionally we collaborate on several projects with:

• Indiana University - Bloomington
• Wageningen University & Research

The COVID-19 pandemic has forced us to research at faster rates than ever before to make appropriate decisions. Even though several investigations about the SARS-CoV-2 have been carried out, the role of inert surfaces remains unexplored.

As we mentioned before, in Ecuador, the major barriers to overcome are funding and technological limitations. Submitting this solution to The Trinity Challenge, and being funded, represents a real opportunity to carry out this novel investigation. Furthermore, a potential association with The Trinity Challenge members will allow us to establish partnerships in order to overcome our technological barrier. We will need assistance implementing cutting-edge technologies for virome sequencing in our country, and we hope to connect with other researchers for troubleshooting and recommendations. 

In Ecuador specifically, data needed for decision-making is lacking. We believe our research would be an important step in the right direction towards acquiring new, valuable, and much-needed information. The potential results of this research will be useful in our country for pandemic prevention, preparedness, and management.

Potential partners for our solution are Trinity Challenge Member organizations such as the Global Virome Project and Bill and Melinda Gates Foundation. We propose sharing and learning about research experiences and new strategies with them to enrich our future viral-related projects. Moreover, a potential research/work team between our affiliated institution and the University of Cambridge or the Imperial College London would be ideal to carry out associated investigations.

We will also look to associate with other Ecuadorian universities (at least one from each Ecuadorian principal cities) to fulfill three goals:

1. Increase our sampling scope.
2. Determine the distribution and prevalence of SARS-CoV-2 on inert surfaces in smaller Ecuadorian cities (ideally, where these universities are located).
3. Describe the viral diversity in these cities.

In this way, we will be able to set up a solid beginning which will constitute a small but important step in the study of viral diversity on inert surfaces.