Team:ECUST China/Description
In 2020, the COVID-19 caused by a coronavirus shocked the human world. This is the epidemic that has the greatest impact on human society since the 20th century, covering almost all areas where humans live. Up to now, the coronavirus epidemic has more than 38 million confirmed cases and approximately 1 million people died. The average diagnosis rate has exceeded 0.5% and the average mortality after being infected is about 2.8%, which means that on average, five out of every thousand humans are infected with COVID-19, and three out of every 100 infected people will lose their lives permanently.
The reason why this coronavirus can cause such great damage to human society is that it is highly contagious and extremely concealed. The coronavirus can spread all around the world through direct transmission, aerosol transmission, and droplet transmission. Since the patients will not have typical symptoms for 3 to 7 days (up to 14 days) after infection, this period is called the incubation period. Patients in the incubation period have no difference from ordinary people, but they can still spread the virus. What’s more frightening is that some infected do not show symptoms for a long time, but can continue to infect others. This kind of person is considered to be asymptomatic. With characteristics of high concealment and high transmission, the coronavirus is like an agile assassin, wandering in human society and posing a huge threat to everyone's life and health.
The existence of incubation period and the asymptomatic infections make the diagnosis and isolation based on the occurrence of symptoms insufficient to suppress the spread of the epidemic. To find patients in the incubation period or the asymptomatic, it is necessary to apply epidemiological big data. Infectors are tested and isolated if confirmed, to deter the further spread of the virus. The mainstream detection method is nucleic acid detection, which relies on RT -PCR technology. This detection method requires the design of specialized primers to identify the conserved sequences in the coronavirus genome, therefore, there’s a restriction that the target sequence does not undergo mutations.
However, the coronavirus can not only “sneak”, but also “change the face”. As an RNA virus, its genome sequence is very vulnerable to mutations, especially at the beginning of the epidemic outbreak. Due to the founder effect, many sporadic mutations are inherited by a large number of offsprings, which accelerates the alienation between different viruses. For example, an early study found that the coronavirus can be divided into two lineages by mutations at the two sites of 8782 and 28144, and these two lineages derived many other different lineages in the subsequent development. If these mutations happen to occur in the target sequence of the specific primer, it will result in false-negative results. Therefore, in actual operation, multiple pairs of primers are often used to detect samples. The problem of mutation not only reduces the accuracy of detection but also greatly increases the workload of detection.
The sudden outbreak of the coronavirus epidemic, unfortunately, separated the ECUST_China team members. Facing the increasingly serious epidemic and in a sense of mission as an iGEMer, we hope to contribute our strength to the world's fight against the coronavirus. Meanwhile, there happened a thing that triggered our thinking about the detection of coronavirus.
Due to the epidemic, one of our team members was trapped in the school and could not go home. In the lonely school life, he got some symptoms such as fever and cough, so he went to the hospital immediately. The initial test result from the hospital was positive for coronavirus pneumonia, which made him extremely disappointed. After a short period of isolation, he did the second test and was told that the previous test result was a misdiagnosis. What he got was not coronavirus pneumonia, but just common pneumonia. This misdiagnosis made him feel that the existing detection methods have many shortcomings and the idea of developing a more efficient detection method was born. After other iGEMer learned of this, they also decided to support his idea, so our team moved on to develop a new detection method.
As mentioned in the background, the coronavirus’s ability to "sneak " and "change faces" make its detection more difficult. Therefore, we carried out an online survey in March, whose results show that patients should wait for one day to three days in duration to get the test results, and some patients wait for more than 4 days. In the analysis of the mainstream RT-PCR nucleic acid detection method, we found that it exists some problems such as it has low accuracy, cannot detect mutations, and takes a long time. Moreover, the RT-PCR operation requires professional equipment and personnel, which will lead to the concentration of testing resources and then increase the work pressure of the testing personnel and their risk of infection.
We have designed a POCT detection device which is more convenient, faster, more accurate, and capable of detecting mutations. It can complete the entire detection process within two hours, and output electrical signals that can be viewed on a mobile phone. This equipment can be used for testing in homes and communities so that everyone in need of testing can quickly get their test results. It will play the role of a smart "detective" to find out the hard-to-find coronavirus. Its name is D-E-tector.
D-E-Tector is a new POCT detecting device, which combines the advantages of nanomachines, electrochemical, and digital microfluidics, to achieve an automatic and high-throughput detection. In our design, the sample input flows on the DMF platform in the form of droplets. Each droplet firstly reaches the DNA Walker reaction zone for signal amplification and then arrived at the E-CRISPR reaction zone to complete a conversion from a chemical signal to an electrical one. The electrochemical workstation’s Bluetooth module will transmit the signal to the testers’ cell phone to realize the visualization of the signal.
D-E-tector not only enables the detection of coronavirus but also realize the detection at different sites by simply changing the identification region of DNA Walker. In other words, we only need to design different identification sequences for different viruses, and then the D-E-tector can realize the detection of them, even one false base in the sequence will be reflected in the output, which gives it an ability to detect mutations. By designing identification sequences for different viruses and mutations at different sites, and using the advantages of digital microfluidics to achieve multi-channel simultaneous detection, it is possible to detect multiple viruses and target site mutations at the same time in a single detection.
Besides, D-E-Tector’s volume is less than 2 dm3, which means that it can be easily transported to wherever it is needed. Moreover, by replacing the disposable electrode, DNA Walker suspensions, and the fluid carrier plate, it can be repeatedly used. The whole detection process does not require a professional operation. People can just use the routine sampling method to obtain the sample and input it into the machine, and the detection can be completed through the set program. The whole process does not exceed two hour. We hope to control the single detection cost within 150 RMB, making it a portable detection device that is suitable for families and communities.
reference:
[1] CHU DKW,PAN Y,CHENG SMS,et al.Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia[J/OL]. ClinChem.(2020-01-31)[2020-02-21].
[2] Xiaolu Tang, Changcheng Wu, Xiang Li, Yuhe Song, Xinmin Yao, Xinkai Wu, Yuange Duan, Hong Zhang, Yirong Wang, Zhaohui Qian, Jie Cui, Jian Lu, On the origin and continuing evolution of SARS-CoV-2, National Science Review, Volume 7, Issue 6, June 2020, Pages 1012–1023.
[3] Oscar A MacLean, Richard J Orton, Joshua B Singer, David L Robertson, No evidence for distinct types in the evolution of SARS-CoV-2, Virus Evolution, Volume 6, Issue 1, January 2020, veaa034.
[4] Forster, P. et al. (2020) ‘Phylogenetic Network Analysis of SARS-CoV-2 Genomes‘, Proceedings of the National Academy of Sciences of the United States of America. Doi: 10.1073/pnas.2004999117.
[5] Liang C P , Ma P Q , Liu H , et al. Rational Engineering of a Dynamic, Entropy‐Driven DNA Nanomachine for Intracellular MicroRNA Imaging[J]. Angewandte Chemie, 2017.
[6] Dai Y , Somoza R A , Wang L , et al. Exploring the Trans‐Cleavage Activity of CRISPR‐Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor[J]. Angewandte Chemie International Edition, 2019, 58(48).
[7] Xu W , Jin T , Dai Y , et al. Surpassing the detection limit and accuracy of the electrochemical DNA sensor through the application of CRISPR Cas systems[J]. Biosensors & Bioelectronics, 2020, 155:112100.