DESCRIPTION
Background
The SARS-CoV-2 has been wreaking havoc for three years,which has made humanity lost too much. Many people have lost their jobs, some have developed depressive symptoms because of it, and some children have lost their sheltered families, even some elderly people have died from being neglect or starvation in their homes[1].
Figure1. A white flag 2021 with words to honor loved ones is seen on a lawn near the Washington Monument in Washington, DC, Sept. 17,2021. Photo by Xinhua News Agency reporter Jie Liu
Just when we thought the fog of the epidemic was finally lifting, the SARS-CoV-2 was always able to mutate new variants that would elude the human immune system. To date, there have been hundreds of variants of the SARS-CoV-2[2].
Figure2. The evolutionary tree of SARS-CoV-2 and representative common coronavirus strains that infect humans. Those coronaviruses could be grouped into 3 clades[2].
They had better disguising which can help them escape the immune response, or even reduce the effect of the vaccine[3]. The epidemic is still spreading around the world because humans can not develop a vaccine as quickly as they can.
Now, although people are returning to normal life, the bigger bad news is that wildlife habitat is being destroyed by climate change. This allows many wildlife habitats to overlap with anthropic zone, which increases the chances of zoonosis. Perhaps in the future, we need to deal with more complex infectious diseases, things will be more complicated then[4]. So are we really ready for the next one? What exactly should we learn from this outbreak?
Here, the FAFU's answer is that we should identify and intervene epidemic in some areas as early as possible.
Inspiration
We discussed all of igem’s projects studying the topic of COVID-19 during the preliminary phase of data collection,and we found that almost all teams chose nucleic acid detection methods. However, detection of nucleic acid as a coronavirus in the case of COVID-19 requires virus lysing, which increases the workload of the testers. So we chose the method of antigen detection. After that we got to know about sewage epidemiology. We all felt that sewage is a good vehicle for detection. Because all people need water to live, biological information is released into the sewage along with the water. Then the detection of domestic sewage can efficiently determine whether the area is infected with the virus. In order to construct the whole system, we divided the whole project into three stages: enrichment of viruses, detection of viruses and construction of the whole device.
Wastewater epidemiology
Through the detection of pathogens in wastewater, people can predict the potential outbreak of epidemic diseases in cities. In Japan and Israel, poliovirus, hepatitis virus and SARS-CoV-2 were detected in wastewater, and the further spread was prevented early in the outbreak.
Studies have shown that the SARS-CoV-2 can also infect small intestinal epithelial cells [5] , causing diarrhea in infected people. These viruses are released into the city's wastewater system along with domestic wastewater.
At present, wastewater epidemiology is also used in the local epidemic warning and dynamic monitoring. In the Netherlands and Spain, viral RNA was detected in wastewater more than a dozen days before patient zero was diagnosed[6]. In a French experiment, researchers performed four relatively uniform tests in Paris, and the results showed a good linear correlation with local actual crowns prevalence trends[7]. This proves that we can use the relevant markers in wastewater to predict the trend of local outbreaks.
However, the current wastewater epidemiological testing needs to rely on manual sampling and testing. A great deal of manpower and material resources were expended. Therefore, we want to develop a device that can sample, detect and report on its own, which can reduce the burden of epidemic prevention and control.
Random library
As there are many substances in wastewater, we cannot say that the binding to ACE2 is SARS-CoV-2, that is, the S1 protein subunit. Therefore, we hope to find more proteins that can strongly bind to the S1 protein subunit of SARS-CoV-2 for further verification. Based on this idea, we want to construct a short random peptide library [9] , then we screened the S1 protein subunits of the SARS-CoV-2 to find the peptides that could bind to the S1 protein.
Figure3.Fishing random peptide libraries
Figure4. Yeast Two-Hybrid Systems
Enrichment of Virus
Before we start testing, the first thing we need to do to is to enrich the virus without changing the structure of the virus coat. We came up with the idea of making the virus "stick" to E. coli by anchoring spike-binding peptides on its surface. At the same time, we hope to use light to promote the directed movement of E. coli. We designed two circuits in which E. coli move at high speed in the blue light region and split and die over a period of time, while stagnating in the lightless region.
Figure5. The mechanism by which E. coli "transport" viruses
Detection of Viruses
After obtaining the gripper, we used the PmrAB two-component system as our detection element, which would trigger the sensing mechanism and emit the corresponding intensity of fluorescence when the virus was outside.
We want to use the fluorescence intensity to characterize the concentration of the virus in the sewage in order to estimate the number of infected people in the residential area.Finally, a report will be generated for the epidemic prevention department according to our detecting results. This method will greatly relieve the pressure of early outbreak prevention and control.In addition, we would like to use this device in pandemic isolation sites for external person. With the pandemic scenario, this device could save a significant amount of money in the prevention and control of epidemic in a particular area. We also hope that our project could greatly alleviate the imbalance of development between regions. During the pandemic, we found that the number of infections in some regions exceeded the detection limit at a later stage due to their insufficient detection capacity. We hope that our testing system will alleviate the strain of testing in these countries and provide some reliable data to support the prevention efforts in these countries.
Reference
[1] Liu Suihan, Du Yukai, Gan Yong, Peng Songxu. Factors influencing social support in Chinese population under the background of COVID-19 [J]. Chin J Sociomedin, 222,39(04):408-411.
[2] Zhang Q, Guo HL, Wang J, Zhang Y, Deng PJ, Li FF. Structural Genomic Analysis of SARS-CoV-2 and Other Coronaviruses. Front Genet. 2022 Apr 8;13:801902. doi: 10.3389/fgene.2022.801902. PMID: 35464844; PMCID: PMC9024071.
[3] Mora C, McKenzie T, Gaw IM, Dean JM, von Hammerstein H, Knudson TA, Setter RO, Smith CZ, Webster KM, Patz JA, Franklin EC. Over half of known human pathogenic diseases can be aggravated by climate change. Nat Clim Chang. 2022 Aug 8:1-7. doi: 10.1038/s41558-022-01426-1. Epub ahead of print. PMID: 35968032; PMCID: PMC9362357.
[4] Gao QY, Chen YX, Fang JY. 2019 Novel coronavirus infection and gastrointestinal tract. J Dig Dis. 2020 Mar;21(3):125-126. doi: 10.1111/1751-2980.12851. Epub 2020 Mar 10. PMID: 32096611; PMCID: PMC7162053.
[5] MEDEMA G,HEIJNENL,ELSINGAG,etal. Presence of SARS-Coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in the Netherlands[J]. Environmental Science & Technology Letter,2020,7 (7) : 511-516.
[6] WURTZERS,MARECHALV,MOUCHELJM,etal. Time course quantitative detection of SARS-CoV-2 in Parisian wastewater correlates with COVID-19 confirmed cases [J]. medRxiv,2020. DOI: 10. 1101 /2020. 04. 12. 20062679.
[7] Gangadevi S, Badavath VN, Thakur A, Yin N, De Jonghe S, Acevedo O, Jochmans D, Leyssen P, Wang K, Neyts J, Yujie T, Blum G. Kobophenol A Inhibits Binding of Host ACE2 Receptor with Spike RBD Domain of SARS-CoV-2, a Lead Compound for Blocking COVID-19. J Phys Chem Lett. 2021 Feb 25;12(7):1793-1802. doi: 10.1021/acs.jpclett.0c03119. Epub 2021 Feb 12. PMID: 33577324; PMCID: PMC7901140.
[8] Luan J, Lu Y, Jin X, Zhang L. Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection. Biochem Biophys Res Commun. 2020 May 21;526(1):165-169. doi: 10.1016/j.bbrc.2020.03.047. Epub 2020 Mar 19. PMID: 32201080; PMCID: PMC7102515.
[9] Yang M, Wu Z, Fields S. Protein-peptide interactions analyzed with the yeast two-hybrid system. Nucleic Acids Res. 1995 Apr 11;23(7):1152-6. doi: 10.1093/nar/23.7.1152. PMID: 7739893; PMCID: PMC306824.
