A Call for Global Monitoring COVID-19 to Weaken Its Attack by Combining Sampler, MinION and IOT
Apostle Monoforallogy Moligence1,2,3,4
1. Honghe Health Vocational College (2015-)
2. The First Affiliated Hospital of Chongqing Medical University (2013-2014)
3. Kunming Institute of Zoology, Chinese Academy of Sciences (2010-2013)
4. Sun Yat-sen University (2004-2008)
ABSTRACT: A portable bioaerosol monitor IOT net may help human to deal with COVID-19 and pathogens in future. Author is a probable Asperger who can’t fit the world well enough to gather resource to prove this strategy by himself. After some frustrations, he wish to sound via Nature’s Perspectives and try to help the world through it.
The three musketeers: Sampler, MinION and IOT. Author call globally for anyone who have the resource. To combine them, to save us from COVID-19, you will be messiah!
Coronavirus disease 19 (COVID-19), a pandemic first detected in late 2019. Globally, as of 5:36pm CEST, 13 September 2021, there have been 224,511,226 confirmed cases of COVID-19, including 4,627,540 deaths, reported to WHO[1]. Most of them probably once wished a longer and saner lifetime.
Like predators eat preys, the ability to sense predators always make sense by helping preys shelter away from predators, ultimately predators may die by hunger or killed by warriors from preys.
Despite how small the viruses are, they still are predators in some extent.
If we can monitor the COVID-19 before they reach the concentration to make us affected, we may get rid of them.
Fig. 1. Global pathogen monitoring system drew at 2021-9-22.
I firstly get this insight in late 2020, when London was locked for 4 days before Christmas, quite a lot of truck drivers were blocked on the highway of Dover, and I worried about Robert Plomin in Kings College of London. I wrote quite a lot of manuscripts in my Wechat public account try to let the world see the strategy and make it real.
Unfortunately, as a probable Asperger, my mal-behavior haven’t made the idea spread as my wish, but made me imprisoned in the madhouse for 17 days, due to a misunderstand from police, ruined the Chinese spring festival of quite a lot persons around me, and I find the psychiatric care situation need improvement, both for care giver and receiver.
I spent a few months playing PC game Might and Magic HeroesⅢ to smooth the shock.
Then I try to submit NEJM but the editor said no submission and consideration anymore, you can read it in appendix 1.
Later I paid the entrance ticket and wrote a new manuscript trying to win a lecture in the International Frontier Research and Innovation Forum on Coronavirus, which also failed to get even a sentence of review comment.
I still think the manuscript worth reading, it is as below, and I advice you read the “Reference literatures to prove with zero funding” part first, which may help understand.
Upgrade MinION to Automatic Monitor Net for the Pathogens Invasion
Apostle Moligence1,2,3,4
1. Honghe Health Vocational College (2015-)
2. The First Affiliated Hospital of Chongqing Medical University (2013-2014)
3. Kunming Institute of Zoology, Chinese Academy of Sciences (2010-2013)
4. Sun Yat-sen University (2004-2008)
Purpose: Try to inspire an idea to help optimize the prevention system in the post-epidemic era. When built to a certain scale, the system could answer where the pathogens come from, and provide early warning before invasion, thus early intervention direct to the infection source can be done.
Method: We broaden our thinking, pour reasonable resources, at a reasonable speed, to develop sequencing based pathogens" automatic monitoring devices, reasonable allocate, combine with Internet of things(Internet of people), big data and other technologies, gradually build the library and network, form the new generation of microbial defense system, crack pathogens" stealth skill, precisely monitoring the environmental pathogens before they do evil.
At present, we keep security and early warning through video monitoring system. The principle work in the field of microbes" monitoring and early warning too.
I will discuss following points: Broad spectrum, Resolution, Automation, Minimal maintenance, Network, Intelligent, Traceability, Dual track, Topological allocation, Portability or become automobile accessory of one man vehicle.
Broad spectrum: The conventional method is specific test, which struggled when variation happened. To solve the problem we could seek broad spectrum, morphological observation is significantly less suitable than sequencing to tell species, and Moore"s Law will gradually make sequencing economically accessible. Oxford Nanopore"s MinION is probably the ancestor of future monitoring sequencers. The two major challenges: How to extract nucleic acid without reagent kits, and anchor guiding complex to the sequencing membrane.
Resolution: Depend on purity and coverage the physical extract technique could achieve, and the parameter configuration of the monitoring sequencer, such as the read length, the ratio of the total copies to nanopores in use, the interval time to sample, and the resampling rate in sample, etc. Some techniques that rely on local computing power, such as the ReadUntil technique, can help improve efficiency.
Automation: To sampling different samples(gas, liquid, solid surface) automatically, dust catcher and its different suction heads is a good reference.
Minimal maintenance: Kit extraction turn to physical or other freeloader mode. I think the most consumable component may be the nanopore plus nucleic acid guiding complex membrane.
Networking, Intelligent and Traceability: Require interdisciplinary cooperation, to enable automatic processing of unusual signals, multi-device calibration and cloud alarm. Refer mobile phone"s step counting and movement track recording.
Dual track: The first generation may perform poor and limits its usage to only monitor, but later generations may fit both monitoring and diagnostic usages.
Topological allocation: Under the guidance of mathematical modeling, crowd place, human-animal boundary area.
Become automobile accessory of one man vehicle: Require interdisciplinary cooperation. When one man vehicle system(personal traffic, reside, data terminal and cloud system) is successfully embrace and replace the nowadays cellphone system, the most economical allocation is one per capita with user. By fine tuning, sequencer can also be used to identify infectious pathogens from user, user"s whole genome sequencing and monitor newly emerging mutations. If one man vehicle system is implemented earlier than microbe monitoring device, it may also provide irreplaceable reagents from vehicle source in early days. Besides as an aircraft carrier, it can also share computing power, GPS, wireless communication networking, tire source centrifuge, gas sampling bin, etc. Furthermore, vehicle is more comfortable than mask or gas mask thus suitable for long-time usage,while other sensors on-board can improve the efficiency of epidemiological investigation.
Besides, I prepared the PPT file for the unreachable oral lecture, you can read it in appendix 2.
Then I brought my father as my guardian of psychopath to see the doctor as an official excuse to Beijing in order to attend the forum to pursuit the leader of Chinese CDC to tell him this strategy.
Unfortunately, the repeated outbreaks of COVID-19 made the forum postponed, just 2 days before on-site registration.
Before the event, I went to a few institutes including Reception Department of National Public Complaints and Proposals Administration, which was a dangerous doing, and I understood why these people should be punished: some of them waste common resource not for public interest, just like some literatures have done, they ruined the fame of academia. These all together exhausted my saving with my credit.
So I can’t attend the restart of the forum at this November anymore, if my psychiatrist agree, I could hire somebody in Beijing try to send the file to the leader of CCDC in the forum. But if I can made the idea know to the world before that date, I can save the money to raise my family.
I remembered of my tutor of master degree’s word, a student’s words worth nothing without academic reputation.
I have to change my attitude towards papers. Before, too many reality made me dislike it because it descend to tools to cheat money. I once admired a Russian mathematician who only publish his work on his web page. But life is life.
Lucky thing was that the psychiatrist and some chiefs of my college guaranteed me, I was not sent to the madhouse for the second time which was said probably the last time and can not go out anymore if sent by police, instead I was permitted to work, my position was kindly changed from rehabilitation department to the library, a probably the best position to engage in scholarship than lab, so I have the time resource to try to do this.
In order to prove my strategy and made this manuscript a little more like a paper, second saving time equal to saving lives, third I forget the usage of Endnote both with soft licence probably out of time, I spend 10 working days to full-read 6+ papers, extract and summarize in turn as below, I will tell my reason of reading.
Reference literatures to prove with zero funding
1st paper, in order to know how others utilize MinION to study COVID-19.
Traditional MinION sequencing of COVID-19 require a parallel NGS calibration and quite a lot of kits to accomplish the landscape, which may cost more than 25 hours to do these schedule by hand (summarize of 2).
My thought: we are not to make de novo library, so parallel NGS calibration is not needed. What we need is short sensor time, automation and kits free. I learned from this paper to cite the victim number of COVID-19 at the beginning.
2nd paper, in order to know more method to sequence RNA directly for COVID-19 is an RNA virus.
Currently, two direct methods are used to identify the positions and types of modification in RNA: mass spectrometry and nanopore technology.
The conventional RNA sequencing is misleading; instead, a more accurate term would be complementary DNA (cDNA) sequencing, because RNAs are converted back to DNA by reverse transcription and then sequenced, which may lose the information carried by up to 140 kinds of known modified ribonucleotides.
Although full-length RNA sequencing technique still call for an investment to develop which may will be on the scale of the Human Genome Project (summarize of 3).
My thought: RNA is more fragile than DNA, to obtain enough length before direct sequencing will help us to distinguish different pathogens, the longer the easier to tell. And we just need to get the essential length enough to distinguish different pathogens, the shorter the easier to prepare.
The 140 kinds of known modified ribonucleotides is a resource, we may find a polymer of one type, which can match 4 letters but not amino acid or other impurities with same sedimentation coefficient, it can form the fishhook to gather the strands.
I was touched deeply by author Vivian G. Cheung’s courage although he/she is in Department of Pediatrics not Microbiology, the probably will to save children from COVID-19 made me a strong impression.
I decided my pseudo-paper titled with “A call for...”. Ps. In Chinese, pseudo sound like idiot brain(秀逗) T-T.
3rd paper, in order to see what David Deamer is doing, he is the man to raise the concept of nanopore sequencing, and I still thought to prepare the library without kits was too hard, after I read through this paper.
This paper told synthesis of nucleic acid strand from two kinds of letters(summarize of 4).
My thought: I often mix up the words kid and kit.
To make monitoring, we need our kids to make kits-free extraction and sequencing in air a reality. Besides, all the workflows should be automatic.
To make our kids survive more through the COVID-19 pandemic, we may need to do it ourselves, some experts of nucleic acid biochemistry like David Deamer may help us find the way to extract and sequence the nucleotide from pathogens in air, but what we need here isn’t synthesis of nucleic acid strand.
4th paper, in order to see how we sample pathogen from air and later tests go.
This paper is a review, which puzzled me: how to cite, hundreds of reference, I won’t read so many to start my writing to save people.
Fortunately, my tutor of master degree replied me: just cite the review.
I paste the sentence without change, so readers can check easier.
This paper is very useful, I advice it to anyone who want to make the pathogen sensor.
Fig. 2. General procedures of airborne virus measurements: sampling and identification.Image modified from (5).My thought: why not detect by ONT(Oxford Nanopore Technologies) after extraction of RNA/DNA? ONT delivered its first commercial device at 2014.
Fig. 3. Schematics of several air samplers used in studies on airborne viruses. Image modified from (5). My thought: we probably have to do much change about the sampler to extract the inner DNA/RNA, because previous samplers were designed to keep the viruses’ vitality.
Although the MID of SARS-CoV-2 in humans needs more research, it is expected to be approximately 100 virus particles (5).
My thought: the sensor must alert us before the danger is serious enough to made us infected. Here, MID = minimum infective doses. Theoretically speaking, nanopore sequencing can detect even one copy of nucleic acid strand once it pass through the nanopore and the current change was recorded.
Since the concentrations of viruses in air are generally very low, the measurement system needs effective concentration techniques for the viruses without causing physical/biological damage, and/or the LOD of the measurement system should be low enough to detect the virus concentration robustly and stably. The minimum detectable virus concentration in air is related to the enrichment ratio (ER) of a sampler and the LOD of the measurement system (5).
My thought: the damages may not so important if a nanopore sequencing following directly. Impactors first choice and water-condensation-based samplers which can increase the physical collection efficiency of small virus particles may work after monocar system come true. Here, LOD = limits of detection.
Environmental stress such as ambient temperature and humidity, ROS, and UV light, as well as aerosol generation and sampling can cause physical and biological damage to certain parts of the viruses, e.g., nucleic acids and surface/inner proteins, resulting in loss of viability (5).
My thought: what we have to find is a diet which can erase the surface and inner proteins of pathogens with least damage to nucleic acid.
We have to know some kind of virus such as Marseillevirus has histone doublet which may become complicated when we are going to make it a broad spectrum sensor.
Microbe such as Deinococcus radiodurans who survive under 5kGy radiation may become a reference marker if we use radiation but I prefer not. Sadly, I don’t know which microorganism can resist the strongest wind/tear force to become marker when we develop this sensor.
And I can’t stop to think of the scene of Marilyn Monroe and Flowers & Snake: the wind curled the cloth (capsid, envelop etc.) outside, with a lash (strings which can adhere the cloth) to tear apart the cloth we do not need...Oh, man!
A few studies have attempted an integrated detection system with air samplers for rapid on-site detection. Try to shorter the testing time. Usachev and Agranovski (Usachev and Agranovski, 2012) detected T4 bacteriophages using personal air samplers integrated with qPCR by loading all the reagents into collection media before qPCR without need for RNA purification. The total measurement time including sampling was 70 min (sampling: 10 min and qPCR: 1 h), and the LOD was 24 PFUs per reaction. Agranovski et al. (2017) developed a miniature real-time PCR-based portable bioaerosol monitoring system; this system can detect within 30–80 min on-site for aerosol particles larger than 0.2 μm, and the PCR analysis commenced after certain abnormal signals were observed (5).
My thought: wow! Direct testing without need for RNA purification?! That’s what I’m looking for. But PCR always ask for kits like ammo or film cassettes, a monitor must work quite a lot of runs without intervention.
Until now, most of these techniques have not been fully applied for field detection owing to experimental difficulties in working with real bioaerosols, such as low concentrations of the viral aerosols as well as potential virus damage during the sampling process (5).
My thought: this review was received 17 April 2021. Are they wait for me to give me the chance to gain a great fame?
Yes, when I tried to talk with venerable men, at the cost of years and about 7k dollars in total, I finally find fame earn the respect to make communication work, when only the man at the right position can gather resource and lead people, to persuade him, fame is more important than knowledge, just think about John Nash. The title you get from madhouse may change to the opposite, but before that, it’s a bad title: the film
After famed, it may become easier to made monocar system real, then moligence and true unification of human being may come true, which may made it easier to let us become multiplanet species.
I have talked quite a lot about monocar system (I call it wheelonging project) in my Wechat public account in Chinese. In fact, the sensor of pathogen is an automobile accessory of the proposed system. You can sweep the QR code in appendix 3 by APP Wechat, but the files are almost Chinese version.
Microfluidic platforms have been recently used for bioaerosol detection for serial processes of air sampling, waterborne sample transport, and bioassay to enhance detection sensitivity, to obtain rapid assays, and for continuous monitoring, etc. (Huffman et al., 2019).
However, no microfluidic devices are commercially available for bioaerosols until now despite the potential and laboratory-level demonstrations of microfluidic-coupled bioaerosol detection (King et al., 2020; Huffman et al., 2019).
Moreover, the integration of nanosensors with microfluidic technologies is a promising approach for bioaerosol measurements; however, it is not easy to guide and capture the target analytes on a small detection area, and the stability and lifetime of an antibody-based nanosensor can deteriorate when exposed to environmental conditions (5).
My thought: think about river delta, water and wind all follow hydromechanics. The same as mass spectrum, cascade impactor and cyclone, things of one kind come together, we just have to find the right spot in space and use a little pool of maybe electrostatic water to fetch them, if there are durable, electrical variable, nucleic acid specific fishhook... The lance (strand of nucleic acid) of Don Quixote into the circled (work and reset) windmill.
Rapid on-site measurement of airborne viruses is highly required to prevent the spread of air-transmissible diseases at early stages.
Airborne virus measurement typically consists of two processes: air sampling and virus measurement. Therefore, reliable sampling of airborne viruses along with advanced measurement techniques is critical to effectively measure airborne viruses. To date, many sampling devices and techniques have been presented. However, a portable sampler that meets all the requirements of large flowrate sampling, biologically safe virus collection, high ER, and high collection efficiency for particles ranging from tens of nanometers to tens of micrometers in size remains a challenge; hence, only a limited information about airborne viruses is known.
Since the number of viruses in the air is very small, and there exist many non-target particles such as particulate matter, collected viruses should be purified and/or enriched prior to measurement to reduce false measurements.
From the standpoint of airborne virus measurement, a portable and sensitive real-time measurement system providing species-level specificity can be ideal, but there exist many technical limitations. Therefore, rapid (less than 1–2 h including sampling) unmanned measurement systems that can provide measurement data daily or twice a day are more reasonable and realistic for long-term monitoring purposes, unless viral aerosols of interest require immediate steps or the viral aerosol concentrations vary drastically. Moreover, these monitoring systems suggest that low-cost sensors should be used since long-term measurement may need a great many analytes and analysis time.
My thought: I am very glad to read the underlined conclusion. This review just tell us the sampling part, I have to find more detail of measurement by ONT. Can rhodium catalyst which make oxygen and nitrogen divorce do some help on library preparing? Besides, made the sensor an Internet of Things (IOT) will help us to realize global remote sense.
5th paper, in order to see how direct testing without need for RNA purification can work.
A portable bioaerosol monitor is greatly demanded technology in many areas including air quality control, occupational exposure assessment and health risk evaluation, environmental studies and, especially, in defence and bio-terrorism applications (6).
My thought: I can’t agree more and grate more to see this work. I searched the author I.E.Agranovski, and found his 20 more years of chasing for a portable bioaerosol monitor of pathogen. I express my respect by exhibiting his portrait which I found from the book he wrote:
Fig. 4. Igor E. Agranovski, Ph.D., Professor
Griffith School of Engineering
Griffith University, Brisbane
Australia
(Without permission)
To minimize reagent consumption and idle running of the technology, an event of a bioaerosol burst is confirmed by three parameters: aerosol particle size, concentration and composition (6).
My thought: it is just like event related potential (ERP) in psychology. But in my design, we haven’t to set this trigger. We made some amount of anchored adaptors which can move in a range, when they are all coupled with strand, the pool change place windmilling which made the sequencing start. The time span of coupling would recorded to assess the concentration in bioaerosol.
Due to recent outbreaks of infectious airborne diseases and the continuing threat of intentionally released bioaerosol attacks, investigations into the possibility of the early and reliable detection of pathogenic micro-organisms in the air is becoming increasingly important. The proposed technology consisting of a bioaerosol sampler, technology trigger and PCR device is capable of detecting selected airborne micro-organisms on the spot within a short time period (6).
My thought: biological warfare isn’t a good idea because we share too much to distinguish. Still, the IOT of broad spectrum portable bioaerosol monitor will give an end to biological warfare. Even the war shifts to prion mode, nanopore may evolves the ability of amino sequencing to peaceful it.
Why can’t we communicate to keep peace and unification. There are handicaps to hinder, just think of myself, think of Ignaz Semmelweis who advocated hand washing among obstetricians, how could kind hearts ended in madhouse. Maybe brain wave communication...
Bioaerosols in occupational and residential environments generally represent complex mixtures that may include micro-organisms (viable and dead) as well as their fragments and toxins (Douwes et al. 2003) (6).
My thought: the sensor I call for invention just focus on nucleic acid strand. If there is no mechanism (maybe shorter fragment due to died a long time) to distinguish dead from viable, the false positive alarm may become a concern. The sensor can’t work for the situation of non-nucleic acid toxins either. And we have to find a mechanism to attenuate the interference of non-nucleic acid when sequencing. If we can’t purify without kits, how about give a parallel way to let them go?
The personal sampler was charged with 40 ml of 1× PBS (phosphate-buffered solution, pH = 7.4) and placed in a 60 l aerosol chamber along with the particle concentration trigger (PCT) module, described further in the text.
Upon detection of the concentration burst by the PCT module, the sampler was operated for 5 min, and on completion, a small portion of the collecting liquid from the device (approx. 12 μl) was automatically pumped into the PCR tube.
In the tube, the aliquot of the sampling liquid was mixed with the microbial target related PCR reagents added there prior to the experiments and underwent real time PCR amplification (6).
My thought: to sequencing in air is wonderful but may not be accomplished in a near future. Gather and sequence the strands may still in liquid, so, the liquid is a concern we have to fix it out. One solution need a tank to fill, fortunately the volume for a run is little, for example, 10ul, and we make a run each hour. It will consume 50.4ml liquid per month taking no account of other factors. Another way may need a design to collect the moisture, using some filters to get rid of things we do not want. It will be a good idea if we tempt to make the sensor a triphibian version. The reaction pool may stay at the bottom part of the mill to make sure enough liquid: working life.
Such outcomes could form a basis for the conclusion that the suggested portable PCR device thermal cycling as well as the optical system have shown satisfactory performance comparable to expensive highly accurate bench-top instrumentation (6).
My thought: as long as predecessor can PCR, it could probably work in nanopore sequencing.
A very important issue related to bioaerosol monitoring is the capability of the technique to identify multiple microbial targets in a single run (6).
My thought: nanopore sequencing can fulfil this mission without fluorescence and PCR reagents, it will be easier and cheaper.
Our previous results have shown that the elimination of nucleic acid isolation and purification steps during sample preparation of simple viruses
does not lead to a significant system sensitivity reduction (Usachev et al. 2012).In our previously developed procedure, the nucleic acids release was ensured by a heating step prior to the amplification procedure. Using this research procedure in the current research demonstrated a very close trend between purified nucleic acids and untreated virus templates, indicating that there is no need for bulky and complicated automation of the nucleic acid isolation and purification step (6).
My thought: is it so simple? What a pity I have no lab, skill and money to try it on MinION. This combination will save our world from the damn COVID-19!
But my wife remind me of taking a good care of myself in order not to be captured by policemen and sent to the madhouse anymore T-T. I call globally for anyone who have the resource, just try it, and tell us the result!
Later, heat or just wind, may decided according to the energy each method costs. And we may have to calculate the relationship between this sensor’s percentage in population and the greenhouse effect, before we equipping it to everyone.
We believe that it would be of particular interest to several sectors, such as: industrial hygiene, environmental health, public health, patient care centres, defence, first responders, hazardous materials teams and military, where the rapid detection of airborne pathogens is of great importance (6).
My thought: Igor E. Agranovski is a lonely prophet, what a pity. If he succeed before, COVID-19 may not happen.
6th paper, in order to see how the enrichment on sequencing level work: sequence which we want, let it go which we do not want. I haven’t read all this paper through because I have read the Chinese version and know some of the nanopore technology before.
The Oxford Nanopore Technologies (ONT) MinION sequencer represents a significant paradigm shift in the reach, applicability, and capability of nucleic acid sequencing technology. Combining a portable form factor, simple library prep, long-read capability (kb to Mb), direct RNA sequencing, and real-time data output, the MinION has been variously applied to forensic genotyping, bacterial typing, plant biology, food safety, environmental metagenomics, cancer research, antibiotic resistance studies and de novo genome assembly. The small operational and logistical footprint of the MinION, combined with its real-time capabilities, make it uniquely suited to diagnostics and surveillance in clinical and feld-forward settings, where the MinION has already been applied to assay Ebola, Zika, tuberculosis, and other pathogens (7).
My thought: as a dwarf in expression, I prefer quoting to saying rubbish by myself, I still wish I could be a good mannered person accepted by the world.
MinION Mk1B is a sequencer of ONT, with a size of length*width*height = 105mm*33mm*23mm, supply voltage = 5V, maximum operating current = 1A, maximum power = 5W, which may not cause a significant greenhouse effect.
Moreover, RUBRIC is specifcally designed to function with the more modest computing resources typical of portable or point-of-need MinION-based activities rather than high-end multiprocessor workstations or cluster computing platforms of Loose’s original dynamic time warping (DTW) algorithm (7).
My thought: the algorithm is important for low computing power. I remembered I have saw the MinION been run in a mobile phone, which can be a portable tool of GPS, timer to form the IOT net.
But the paper seem to be all talking about algorithm later, I didn’t read it through, with the theoretical assumption we can control the direction where the strand will go.
7th paper, in order to see the applications of nanopore technology, this paper is a review too.
Fig. 5. Table from (8), the genome of COVID-19 is about 30k,rough estimate 0.00126 dollar per particle by ONT, and the cost will decline.
Solid-state nanopore...It breaks the limit of natural occurring nanopores and has many advantages, such as very high chemical stability, control of diameter and channel length, adjustable surface properties, and the potential for integration into devices and arrays.
However, the biological nanopores are frail with features such as short lifetime, intrinsic instability, and strict requirement of a specific environment, which are not able to support a biosensor’s long-term operations.
MinION could only generate 50 Gb within 72-h operation (8).
My thought: considering the harsh situation, solid-state nanopore may win which may suffer a lower accuracy at the beginning, don’t worry, read back the “Dual track” part, it’s a to customer and surveillant design not a to business and diagnostic design.
The quantity of nanopores can change according to demands, we haven’t to conjunct MinION directly, we just conjunct the nanopore technology after sampling. The requiring computing power may change consequently.
The reaction system for nanopore sequencing is carried out in a flow cell, in which two ionic solution-filled compartments were separated by membranes containing either 2048 (MinION) or 12,000 (PromethION) nanopores. The process of nanopore gene sequencing can be divided into three parts, library preparation, sequencing process, and Basecaller.
The nanopore technology can be used to sequence the DNA or RNA sequence of microbes, and it helps researchers to classify or monitor the microbes. Moreover, it is promising to establish microbe surveillance and response quickly during pandemic, if the nanopore technology can be applied in the area of public health.
It weighs less than 100 g and is easy to operate in developing countries where the experimental condition cannot be achieved.
Among them, Wang et al. proposed a nanopore targeted sequencing (NTS) technology to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6–10 h. Researchers proved that NTS can effectively monitor the mutation of nucleic acid sequences, categorize the type of SARS-CoV-2 and other respiratory viruses in the samples.
In the future,nanopore sequencing technology will be continuously optimized from the structure of nanopore, machine algorithm of basecalling, and new methods of library preparation (8).
My thought: empty talk spoils a county; solid work prospers it. You may draw a better draft than me after reading and make it real.
Others
A paper on MedRivx: Cecilia A. Sánchez, et al. may help us to realize the importance of the sensor discussed here, and to think of its topological allocation. I just have read its Chinese short comment in Wechat, I think this can’t be a reference which I haven’t read.
I add with some technical question from part of a message to ONT staff which may help. You can get them in appendix 4, but it is a Chinese version.
My draft about the device
Threshing-winnowing machine, cochlea, waterwheel loaded with nucleic acid strands, handheld water ring game machine, voltage gated ion channel, colloidal gold adsorption, Bernoulli effect, wind & solar energy, pressure of wind to keep the wheel below the water level of the tank, gasoline engine.
Fig. 6. Another draft I drew.
Fig. 7. A poster I drew.
SUMMARY
The COVID-19 may urge the sequencing technology advancing to next generations which represent kits-free to realize monitoring. The future may repeat the history of photography industry: cartridges to CCDs. Pioneer who can draw strength from state power may become the industry giant in future. The three musketeers: Sampler, MinION and IOT. To combine them, to save us from COVID-19, you will be messiah!
References
You can get them in appendix 5.
[1]World Health Organization. WHO Coronavirus (COVID-19) Dashboard
(13 September 2021). Available at: https://covid19.who.int/Accessed 14 September 2021.
[2]Andreas Walker, et al. Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting. Clinical Infectious Diseases 2021; XX(XX):1-8.
[3]Juan D. Alfonzo, et al. A call for direct sequencing of full-length RNAs to identify all modifcations. Nature Genetics 2021; 53: 1113-1116.
[4]Tue Hassenkam, et al. AFM Images of Viroid-Sized Rings That Self-Assemble from Mononucleotides through Wet–Dry Cycling: Implications for the Origin of Life. Life 2020; 10: 321.
[5]Jyoti Bhardwaj, et al. Recent advancements in the measurement of pathogenic airborne viruses. Journal of Hazardous Materials 2021; 420: 126574.
[6]I.E. Agranovski, et al. Miniature PCR based portable bioaerosol monitor development. Journal of Applied Microbiology 2016; 122: 129-138.
[7]Harrison S. Edwards, et al. Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria. Natureresearch Scientific Reports 2019; 9:11475
[8]Bo Lin, et al. Nanopore Technology and Its Applications in Gene Sequencing. Biosensors 2021; 11: 214.
