May 8, 2020 | Adamas University

CRISPR tool based detection of Covid-19 Final

A novel, quicker and economical ‘Dip-strip’ methods of Covid-19 detection based on CRISPR technology: The limitless scope of research in the Biotechnology sector

Student Contributor: Sayantan Das & Srijit Bera (B.Sc Biotechnology Sem-VI)

The landscape of Covid-19: Since December 2019, the Covid-19 has affected more than 3.5 million individuals globally with a case-fatality rate of more than 6% (data taken up to 30^th April 2020) reported. Experience from China, Italy, UK, France, and the USA demonstrated that Covid-19 can overwhelm even the healthcare capacities of well-resourced countries where man-to-man disease transmission has been reported with mild or no symptoms.

The challenges: The biggest problem is that the virus is evolving continuously and several varieties have already been identified by scientists all over the world. Since there were no gold standard medicinal treatments available to date, interventions have focused only on contact tracing, quarantine, and physical distancing.

Since the initial pandemic wave, few countries like India have implemented physical distancing measures as a mandate according to the China model. Furthermore, in each time this emerging viral threat has hindered the public health response due to a lack of rapid, accurate, and accessible molecular diagnostics. However, whether the virus can potentially be transmitted in other ways than by respiratory droplets is still unknown to scientists.

Present detection: This has to be noted that this novel coronavirus (SARS-CoV-2) is a positive-stranded RNA virus. Hence, the Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) of nasopharyngeal or oropharyngeal swabs typically has been used to confirm the presence of this virus and recommended by several laboratories, including the CDC and WHO. RT-PCR tests are rather quick, sensitive and can produce results in 3 to 4 hours, although this usually takes much longer time when samples are to be sent to specialized external laboratories (6-8 hours on average).

Though serological tests are fast and need minimal equipment but their usefulness might be limited for diagnosis of acute SARS-CoV-2 infection as it may take a couple of days to weeks following the start of symptoms in patients to get a measurable antibody response. The Rapid Diagnostic Test (RDT) is an immunoassay test that detects viral proteins (antigens) (Figure 1). Though this technique is fast but evidentially, it gives negative results for some cases. Moreover, RDTs can be damaged by heat and humidity, so an RDT should not be removed from its sealed packet until right before you are ready to use it otherwise it may show an invalid (false) result. Hence, there was an urgent need globally to develop a rapid testing tool for diagnostics.

The alternative: Among all the temporary procedures for virus detection, CRISPR based detection of microbial DNA/RNA has provided a quicker and economical alternative to RDT and RT-PCR. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a type of DNA sequence found in bacteria when they are previously infected by a specific variety of viruses called ‘bacteriophages’ to reproduce. Hence, these sequences are considered to be the anti-phage (i.e. antiviral) defense system of bacteria (or immune system for bacteria against phage viruses). The CRISPR mechanism relies on the guide RNA finding its complementary target sequence and the commonly used Cas9 nuclease (a type of molecular scissors) is cutting at the precise site. Together with CRISPR-associated proteins (or Cas), this “CRISPR-Cas” cutting-edge technology has been stated using to edit genes within organisms, development of biotechnology products, correcting genetic defects, improving crops, detection, and treatment of diseases and many more with immense scope of research for biotechnologists in India and abroad.

The DETECTIVES for Covid-19 detection:

The SHERLOCK Technology for Coronavirus Detection:

In 2017, Feng Zhang’s group from the USA first reported a CRISPR-based nucleic acid detection technique called SHERLOCK (Specific High sensitivity Enzymatic Reporter unLOCKing). In their latest research came in February 2020, they targeted two genes (S gene and Orf1ab) from the SARS-CoV-2 genome.

The SHERLOCK detection technique for Covid-19 detection involves three steps:

Firstly, the amplification of the viral RNA using recombinase polymerase amplification (RPA) technique followed by in vitro transcription of amplified DNA back into RNA.
Secondly, they detected viral RNA using Cas13 nuclease and Synthego-supplied crRNA (CRISPR RNA) targeting specific sequences.
Finally, they could read out the visual color change using a commercially-available paper dip-strip, which captures the cleaved RNA with labeled ends on specific antibody bands.

These two nucleases (Cas12a and Cas13a) have become popular in CRISPR diagnostics while Cas12a is DNA-specific, Cas13a works with RNA. An interesting feature of Cas12 and Cas13 nucleases is that they showed collateral cutting activity. On finding the target, the nucleases will cut other non-targeted nucleic acid molecules in the vicinity as well.

The researchers demonstrated that they could use this protocol to detect coronavirus RNA sequences with a sensitivity of 10-100 copies/microliter of the input sample. They note that this technology can be used for testing RNA purified from patient samples in ‘less than an hour’ without the need for special instrumentation like real-time PCR.

The DETECTR Technology for Coronavirus Detection:

In 2018, Mammoth Biosciences reported a new method named DETECTR (DNA Endonuclease-Targeted CRISPR Trans Reporter), for sensitive DNA detection using Cas12a nuclease. In March 2020, Mammoth Biosciences published a report on how the DETECTR platform could be adapted to detect SARS-CoV-2 RNA in just 30 minutes. Such a rapid diagnostic platform would be particularly valuable in high-risk areas.

The DETECTR detection protocol for Covid-19 virus detection involves following steps:

Amplification of the RNA extracted from the sample using reverse transcription loop-mediated isothermal amplification (RT-LAMP) technique followed by Cas12a-based detection for viral N gene and E gene.
Detection of DNA using Cas12a and Synthego-supplied crRNA targeting specific sequences.
Visual readout using commercially available dip-strips. In the lateral flow-strip assay, a positive result will detect at least one of the two SARS-CoV-2 viral gene targets (N gene or E gene).

Comparing their methods to the SHERLOCK-based protocol, the Mammoth Biosciences team noted that their platform enabled faster detection (30 instead of 60 minutes) as they saved the time spent on the additional IVT (in vitro transcription) steps required for Cas13a-based detection. These techniques could detect Covid-19 much faster than the conventional RT-PCR technique (Figure 2).

Figure 2: Comparison between these three techniques for the detection of SARS-CoV-2

Where we are?

India had always nurtured creative research minds who always came up with a solution in the time of crisis. Recently, the scientists at the CSIR-IGIB have also developed a quicker (take less than 40 minutes for detection) and economical (~Rs. 500/- per sample detection) with high accuracy CRISPR based method that will not require any expensive machines for detection of SARS-CoV-2. They named their invention “FELUDA”, the detective character introduced by the legendary filmmaker Satyajit Ray. The CRISPR-FnCas9 based Dip-strips tests have been developed by the team members of Dr. Debojyoti Chakraborty and Dr. Souvik Maity as a simpler way of detecting SARS-CoV-2.

“Necessity is the Mother of Invention”.

In conclusion, I must say that in India, both in the government and private sectors the scope of scientific research in the biotechnology field is immense, and probably the sky is the limit. There is an immense need for research professionals in this fast-growing field with great scope for carrier growth.

TO TRAVEL, OR NOT TO TRAVEL: THAT IS THE DILEMMA

‘To be, or not to be’ is a deeply philosophical question that intrigued Hamlet, Prince of Denmark in William Shakespeare’s eponymous tragedy. A similar dilemma stares denizens of the Covid-19 infested global community — right there in the face. To travel, or not to travel — an issue that may have less to do with epistemological musings but definitely with existential imperatives.

In a self-quarantined universe any kind of human concourse has been literally abandoned. Leave alone moon landings and mars missions, rail stations and airports, bus terminuses and cab stations are all sealed off and ‘Not a creature was stirring, not even a mouse’.

Sanitised and disinfected spaces sport a deserted look that makes isolation the name of the game. A lone sentinel keeps guard that the battle lines are indelibly drawn and none ( though one is never sure of the virus itself) can infiltrate into what were, not so long ago, hubs of human mobility.

Travel advisories the world over have ruled out international hobnobbing even for purposes of business in corporate circuits or for exchange of research and knowledge in academia. The current scenario is encouraging virtual meetings over Zoom and Skype that rules out travel and commuting. Webinars have become the order of the day and institutions and organisations are jumping on to the bandwagon cutting out any form of direct encounters that may play havoc with the newly formulated norm of social distancing.

So how do travel businesses, airlines and tour companies handle this unforeseen and unprecedented lock-down? Several airline companies in India have been pulled up for not refunding money to passengers who had to cancel tickets due to the suspension of flights, both domestic and international, since late March 2020. Some others have been given warnings for having announced new passenger bookings even before the central government has lifted the ban on travel.

However one wonders who these die-hard prospective passengers could be, bitten by the wander-lust bug. Or are these people stuck in places of work hankering to be home with family in these times of pandemic? Exiled individuals attempting to make their heroic journey homewards like Odysseus, ignoring the dangers of the journey.

Just as the digital divide is becoming markedly visible in these days of virtual learning, classrooms and communication, patterns of movement have thrown up news and visuals of rural India’s migrant workers caught unawares without work and therefore without food in the cities and urban centres of India. Pangs of hunger, tales of employer’s neglect, travails of marginalisation have compelled them to walk back over hundreds of kilometres, across state borders to reach their village homes. Police action has put them behind bars or led to punitive measures for having broken restrictions and taboos; such migrants have been even forcibly crowded into quarantine camps. Trudging along highways without food and water has caused not just hardship but death for several of these courageous pedestrians on a marathon homeward expedition. These people constitute the nation’s backbone, its grass root level workforce, its senior citizens as also a young populace, future citizens who are yet to come of age in an India to which they belong.

In the pre- Covid world, travel did not refer only to tourism, travel referred to any form of spatial displacement within the context of a specific temporal span. Just as exploratory voyages and maritime trade were considered forms of travel, other manners of journeying and movement on land, including negotiating the rugged terrains and passes in caravans, on mule, camel or horseback along the famed silk route took humans to new places, different cultures, alien ethnicities.

Is Francis Bacon’s maxim in his essay “Of Travel”, widely emulated and followed over centuries that stipulated — “Travel, in the younger sort, is a part of education, in the elder, a part of experience. He that travelleth into a country, before he hath some entrance into the language, goeth to school, and not to travel” — likely to take a double somersault? The motto today being ‘Stay Home, Stay Safe’.

Travel and tourism is a global industry that seems to be gravely compromised now. When it does pick up in the Post- Covid world it is anybody’s guess how things will change. Until the corona vaccine is in place, travel, when the shutdown eases will be severely limited to necessary travel. Patterns of travel are likely to be revolutionised as well as the conditions of travel by air and rail which will need to take corona precautions by modifying seating, strengthening hygiene and ensuring extreme safety measures. The daily commute is likely to be drastically modified with more of work from home options being offered to regular office goers. A paradigm shift in the concept of who travels, why one travels and where one travels will necessarily modify the global perspective of the industry. Leisure travel will be hit badly and the peripatetic Bengali traveller, so ubiquitously present in all tourist destinations on pre-Puja and post-Puja sojourns will reluctantly settle down to life in a ‘home sweet home’. The excitement of being the identifiable Bengali traveller at a tourist destination, so humorously captured in the cartoon below, will become a much cherished memory, experiences that dreams are made of!

#ideaPlus: Decoding The New Normal

Dear Readers,

Thank you for finding us. It’s been a few weeks since the government announced a series of measures to protect us from the Covid-19 outbreak. Since then, our world have been subjected to unprecedented changes and uncertainties. Our world before lockdown almost seem to pale into insignificance compared to the new realities of today’s world. The crisis has forced us to change the way we used to operate and take decisive actions in many areas.

A university is uniquely positioned at the frontier of knowledge and has a duty to pushing the boundaries of knowledge for overall benefit of the society. Both creation and dissemination of knowledge is equally important. At Adamas University, our absolute priority remains bringing quality change in the lives of students in addition to our continuous commitment to impact society positively. We provide numerous platforms for exchange of ideas among our students and faculty members regularly. In an yet another endeavour we intend to bring people from around the globe to discuss the current issues and trends so that our stakeholders – students, parents, industry and society at large are benefitted.

As we know globalization is not a choice, but a reality. Both good and bad comes in a package. In this knowledge era, we as a country can only thrive on research and innovation. And the research driven approach to teaching-learning is bound to transform the classroom discussions into more meaningful outcomes.

Education at Adamas University is not only confined to books or four walls of classrooms rather it’s a holistic one. We call it #educationPlus. We are presenting to you our magazine #ideaPlus which is inspired from our philosophy of #educationPlus. My excitement knows no bounds on this occasion of introducing the very first issue of #ideaPlus, the quarterly magazine of Adamas University. On behalf of the #ideaPlus Editorial Team, I extend a warm welcome to the readership of this magazine. I also take this opportunity to thank our authors, editors and support team, all of whom have volunteered to contribute to the success of the magazine.

In response to the outbreak, the face to face classes had to be temporarily suspended however we were able to completely shift to online teaching learning system almost immediately thanks to our committed tech-savvy faculty colleagues. Our faculty and students have already hit news headlines quite a few times with their spirited achievements.

I strongly believe that we will one day look back at this crisis as a catalyst for positive change in everything around us. I particularly see accelerating innovations in education and allied sectors which will soon be considered as new norm. The impact of this crisis on us as well as on our economy is uncertain however most important is our health and personal wellbeing, and that of our loved ones. I’m sure that we will soon emerge from this crisis and be a better version of ourselves.

Happy reading!

Click Here to view the #ideasPlus Magazine

TEACHING MATHEMATICS – CONCEPT MOTIVATION VS ACTION LEARNING -THE CONTROVERSY!

The key of success is the ability to solve problems- this may be a perfect phrase for the most difficult and necessary subject Mathematics. In the present era of technology, a student need both conceptual and practical exposure of Mathematics. For this purpose the teachers (instructors) has a great role. The subject is compulsory up to class X, and after that, it is optional. However, for today’s world every technological, scientific, venture needs the idea of Mathematics a lot.

For this subject many concepts are needed and a student can easily handle this concept if we, the instructors are able to provide some real world phenomena to them based on that concept. This concept has to be given in the beginner level so that students will used to the situation and they can upgrade their thinking capability and cognitive mind. In college / university level, some open problems and classic results can be introduced to the students, which will motivate not only the student but also the teacher. Future teachers of Mathematics are students now. Hence, action learning or real life problems can be introduced to all levels of students from their higher secondary level. Probably this will grow some craze of Mathematics among them.

Some facts:
For the purely theory oriented subject Mathematics, Some of the following facts are very useful. There is a controversy about the teaching of Mathematics. Some teachers follow the conceptual approach with purely theory oriented teaching and after that the application. Some may try to teach theory based on applications. In any case, the basic idea is to trigger
the cognitive mind of the young students to generate a passion for the subject.

Curiosity– This is the main criteria. Regardless the age of the learner, if
curiosity is there, then learning a subject is very pleasant experience. Normally we have seen the child in primary level is more curious rather that an adult now a days.

Motivation– The curiosity will turn into motivation and this help to grow
people as a high quality professional. Teacher has a great role to motivate students. Especially for an engineering or non-math major student, only teacher can motivatehim/her. Initially the motivation will be technology or some real life facts. How Mathematics play a role for the real life problems, if we can able to make a student understand, that may be enough for motivation. Motivation is a bit more in adult learners rather than primary
level due to the lack of visualization of the future of the topic. For example, teacher can motivate a student for differential equation by introducing a real life problem “Vibration of a string” or “Population scenario”.

Deep Learning– For a motivated student, reward does not matter. Sometimes they work for the sake of their passion towards the subject. Students through deep learning try to get the complete knowledge for Mathematics. This will reduce the anxiety among them related to the topic. This can be done through asking questions, drawing diagrams, preparing charts etc.

Real life problems– The common question from student is that “What is the
application in real world?” This question is valid also. For some of the topics in Mathematics (Pure Mathematics), giving a practical example is a challenge. However, for remaining part of Mathematics, we can give some real life problems easily and justify the concept. For example, we can give a pry-predator situation from biological aspect and easily generate some simplified model using differential equation. In optimization we can give the example of work of a delivery boy in a day and how to optimize that properly which leads us to travelling salesman problems in LPP.

Software/ Practical– Now a days, many software are available in the market
to do our job easier. Using MATLAB, MATHEMATICA finding eigen value, characteristic equations, graph generations are very easy and students will be attached to the subject through this. Even in mobiles, we can have various apps of Mathematics, which will make the subject easier for student. Situation of Mathematics in India: Manjul Bhargava, mathematics professor at Princeton University and winner of the Fields Medal(2014), one of the highest honors in math, says India can’t hope to lead the fourth
industrial revolution, “If we don’t have strong mathematical talent coming up very soon”
(Source-https://economictimes.indiatimes.com/jobs/mathematics-is-on-decline-in-india-reasonexcessive-focus-on-engineering/articleshow/69938324.cms?from=mdr) .

“Without the math, the procedures may be just experimental, may work sometimes, sometimes not. Only mathematics will tell you under what circumstances it would work,”- Srinivasa Varadhan, mathematics professor at New York University. (Sourcehttps://economictimes.indiatimes.com/jobs/mathematics-is-on-decline-in-india-reason-excessivefocus-on-engineering/articleshow/69938324.cms?from=mdr)
Both these statements are regarding the two very popular topic of modern era, AI (Artificial Intelligence) and ML (Machine Learning) which is the future all over the world as well as in India. There are various problems I education of Mathematics in India. Specially the ideology of Pure and Applied Math. This divides the whole scenario of Mathematics in India though actually these two topics are not separated. They are very much interlinked and stand together. The study of higher mathematics will be incomplete without the help of research, which is missing in this part of the world. Here we consider teaching and research are two separate quantity.

Action Learning: For these problems, Action Learning may give a ray of hope. This is a problem solving approach, which emphasize on a particular problem and that will reflect on the result. The probable best method is to initially focus on particular topics of the attraction of the students.
Action learning is used traditionally in business management, social science, research based problems. However, this can be introduced to teach Mathematics also. Through this action learning, teacher may be able to find the creativity of the student, which was hidden. It will be the job of the teacher to find the hidden talent through this action learning.

The problems in Mathematics is that it’s language is very abstract and in the higher education it is much more complicated, abstract and it has been taught by create a distance with real world problems. Hence, people are unable to visualize mathematics in real life.

For example, 2? = 4 implies ? = 2, because we divide both side by 2 . Actually, this is a concept of field theory. According to field theory as 2 ≠ 0, so it’s inverse exist and we multiply both side by the inverse, which is 1/2.

When some non math major subjects are taught, the applications of Mathematics in their particular fields need to be discussed, which will attract the students towards it. For non major students, Mathematics need to be taught through action learning and then concepts will be developed based on the applications. So we have to follow “middle of the road” policy.

Hence, finally we can say that Action Learning and Conceptual Mathematics is not different and they will be always together. However, probably we need to fix the order for most of the cases. Without concept, there is no progress. Concepts can be gained through action learning and that will remain with us for a long time.

Electrical Engineering – An appealing career option

Electrical Engineering is that branch of engineering that deals with three E’s electricity, electromagnetism and electronics components. Electrical engineers works with varieties of range of equipment ranging from tiny microchips to huge power station generators.

The interest in this branch mainly arises from different circuits that we deal with at our homes. Some people have the habit of opening various components to fix it or just out of curiosity. This is how the interest to become an Electrical Engineer arises in some budding mind.

Why choose to be an Electrical Engineer?

Electrical Engineers are blessing to our society. It is them who made our life so easy now. They improve the way we communicate and continue to enhance our electrical systems. When you have a deep understanding of how electricity works in your home, such as appliances, gadgets, etc., you will be able to apply your knowledge into designing, developing and giving solutions to problems, from small devices to large computers.

Technology is rapidly growing and with that, the role of electrical engineers becomes more important. They are the forefront of developing new technologies in different industries such as robotics, transportation, construction and healthcare. It is the forefront of future technologies.

Some of the most famous personalities in electrical engineering include Thomas Alva Edison for the invention of the electric bulb, Nikola Tesla for the invention for a simple induction motor.

Career Options for an Electrical Engineer

There are many options which an Electrical Engineer can choose as a career. Some of them are enlisted below:

Electrical Engineer: It is the first option that comes to our mind. In this path you will have to evaluate electrical system working by applying the basic electrical knowledge.
Energy Efficiency Engineer: They usually, design, develop, or evaluate energy-related projects or programs to reduce energy costs.
Entrepreneur: You can become a Businessmen.
Electrical Systems Engineer: Research, design, develop, test, or supervise the manufacturing and installation of electrical equipment.
University Professor: This work involves teaching and research.
Circuit designer: Job in this position involves working out the physical form that an electronic circuit will take. Gives a circuit view of the electrical design of the construction of physical circuit.
Design Engineer: A design engineer is a general term that covers multiple engineering disciplines including electrical, mechanical etc. Basically works on the designing end in any given discipline from the overview layout till the complete product.
Drafting technician: Electrical engineers are into this for drafting the electrical side of any appliance.
Distribution planning engineer: This job deals with the electrical planning and layout of the distribution of power to any given location.
Hardware Engineer: Hardware engineers research, design, develop, and test electrical systems and components.
Military engineer: The job description here involves the electrical communication part in the military services.
Network Engineer: A network engineer, also known as network architect, designs and implements electrical networks.
Project Engineer: A project engineer’s responsibilities include schedule preparation, pre-planning and resource forecasting for engineering and other technical activities relating to the project.
Research Engineer: Research Engineers apply their expertise and knowledge to technical projects, finding innovative, cost-effective means to improve research, techniques, procedures, and/or products and technologies.
Robotics Technologist: Robotic technologists use their knowledge of electrical, electronic, and mechanical systems to assist engineers in the development and production of automated equipment.
Technical sales Engineer: They act as the sales team’s technical encyclopedia during the sale, representing the technical aspects of how the product solves specific customer problems. They perform technical presentations for the product.
Technical writer: Like a Content writer or a developer, a technical writer focuses on generating and writing content with its primary focus on the technical aspects.
Test Technician: Their primary duty is to ensure that products perform their proposed functions in a satisfactory manner. For complex products, such as automobiles or computers, test technicians may specialize in monitoring a specific part or set of components.
Toy Designer: Designing electrical toys like a car or a robot or even a gun comes in the primary duties of this career option.
Aircraft Performance Engineer: As an aircraft performance engineer, you would be responsible for applying advanced engineering principles to the design and development of aircraft, in order to ensure that they operate at optimal levels, as safely and efficiently as possible.

Following are some of the Government Organizations that recruit electrical graduates:

National Thermal Power Corporation Limited
National Hydroelectric Power Corporation
Power Grid
Hindustan Petroleum Corporation Limited
Gas Authority of India Limited
Indian Oil Corporation Ltd.
National Fertilizers Limited
State Electricity Board
Bharat Dynamics Limited
Coal India Limited
Indian Railways
Defense Research and Development Organization (DRDO)
Indian Space Research Organization (ISRO)

Following are some of the companies in private sector that hire various skilled electrical engineers:

ABB
Siemens India
Schneider
General Electric
Alstom
KEC International
Sterling & Wilson
Larsen & Toubro (L&T)
Crompton Greaves Limited
Bajaj Electricals Ltd
Jindal Steel & Power Ltd.
Tata Power
HBL Power Systems Limited
Polycab India
Bharat Bijlee

Global Opportunities

Being an electrical engineer opens a lot of opportunities for you, locally and internationally. Many companies outside the country are in need of electrical engineers, and most of them are open in hiring professionals from other countries. Some companies even require you to travel around, so you will be seeing the world while getting paid well. If you are passionate about working overseas, then this is the way to go.

Women and reproductive health, during and beyond covid-19 – A sociological study

The COVID-19 pandemic has had and will continue to have a profound impact on the lives of people across the globe, as well as health and social systems, and national economies. This upheaval will also have a profound impact on access to family planning information and services, as well as sexual and reproductive health more broadly. Thus there is a need to address the possibility of an unintended baby boom among poor and vulnerable groups.

Despite this disruption, the need for family planning will not change. For most women, family planning is critical, basic health care. As health systems shift to prevent and treat people with COVID-19, it is essential they also protect access to family planning services.

Globally, the unmet need for contraception remains too high. It’s estimated that 214 million women and girls are not using modern contraception, despite wanting to avoid pregnancy. And this was before the COVID-19 pandemic, which is set to further derail access to contraception for women and girls around the world.

The International Planned Parenthood Federation (IPPF) surveyed its member associations in 121 countries to produce the largest global dataset so far on how the COVID-19 pandemic is affecting sexual and reproductive healthcare.

“Millions of women and girls across the world now face an even greater challenge in trying to take care of their own health and bodies, “ said IPPF’s Director General Alvaro Bermejo in a statement. “They have needs that cannot wait, but they are facing a lack of time, lack of choice and lack of access to essential services.”

“Unless governments act now, up to 9.5 million vulnerable women and girls risk losing access to our contraception and safe abortion services in 2020 due to the COVID-19 pandemic,” warned the organisation in a statement.

According to this group’s estimates, service disruptions related to COVID-19 in the 37 countries where they operate could lead to an additional 3 million unintended pregnancies, 2.7 million unsafe abortions and 11,000 pregnancy-related deaths.

Interrupted supply chains

Lockdown measures taken globally to respond to COVID-19 are bringing major disruptions to contraceptive supply chains. Large manufacturers of contraceptives in Asia have had to halt production or operate at reduced capacity, and we may see similar developments in other regions as COVID-19 takes hold.

For example, the world’s largest condom producer – Malaysia’s Karex Bhd – which makes one in every five condoms globally, was forced to close for a week in March and only given permission to reopen at 50% capacity. Production of intrauterine device (IUD) in India – a major global producer of IUDs – has come to a standstill with the Indian government also curtailing export of any product containing progesterone, a key component of a number of contraceptives. In addition to this, the closures of borders and other restrictions imposed in the face of COVID-19 further affect the shipping and distribution of commodities.

Delays in the production and delivery of contraceptive supplies at global and national levels will lead to stock outs of supplies, severely impacting contraceptive access.

Obstructed access

Beyond this, at country level, sexual and reproductive health services, staffing and funds may be diverted to support COVID-19 responses, leaving women and girls unable to access contraceptive and other sexual and reproductive health care. Provision of sexual and reproductive health services will also be affected by infection prevention measures, including health workers’ access to personal protective equipment (PPE).

Even where contraceptives are available and continue to be provided through clinics or pharmacies, the impact of COVID-19 on women’s and girls’ lives will curtail their access in multiple other ways. Quarantine measures and mobility restrictions will affect women’s and girls’ ability to seek out contraceptive services. Financial insecurity and additional caregiving burdens brought on by lockdown measures will be further impediments. Marginalized populations will face additional barriers.

Beyond covid-19

Government and NGO should be working to understand the stresses being placed on our doctors and nurses, thus to deliver as much direct support as possible, they should actively monitor the impact of COVID-19 on the supply of contraceptives and other sexual and reproductive health commodities, and to work with partners and manufacturers to do what we cannot do to solely to meet the needs – to ensure continued availability of supplies.

Both government and NGOs should also work to identify opportunities to modernize their service offering to respond to the rapidly changing landscape, with a view to expanding no touch and digital services and self-management of care, and make a strong case for additional resourcing in these challenging times.

National governments, donors and international agencies – to recognize sexual and reproductive healthcare, including contraceptive services, as essential in this crisis, and to take measures to address disruptions in supply chains and ensure continued service provision at different levels.

If women, girls and marginalized communities cannot access contraceptive care in this crisis, we can expect to see a rise in unintended and forced pregnancies, an increase in sexually transmitted infections, including HIV, and, ultimately, a sharp rise in unsafe abortions. The impacts on women’s and girls’ lives now, and beyond this crisis, will be unthinkably severe.

Strategic Pathways towards COVID-19 diagnosis & treatment

Student contributors – Rahul Dutta, Shaurav Bhattacharyya, Aniket Das ( 3^rd year B. Tech Biotechnology)

The World is witnessing an era where the tiniest being, a mere virus, has taken control over the so-called intelligent minds. Is this the curse of the Almighty or the action of the Evil is not known but what is known is that we must win over this battle to save the innocent human hearts who are becoming victims in the hands of this deadly virus. In recent years, the world is seeing a surge in large-scale epidemics from emerging viruses (like MERS, Ebola & the present SARS-CoV-2) and it is seen that the initial zoonotic animal-to-human transmission event is involved significantly in all of these epidemics. Each time, the viral threat is glorified by the lack of rapid diagnostic testing and quick treatments to obstruct the spread thus hindering public health. The scientists and researchers at every corner of the globe are working relentlessly to find a solution at least to curtail the steep progressive curve of the no. of deaths until the proper vaccine is successfully developed. Here, we are presenting some of the directions in which the scientists are trying to find a way to combat the present crisis scenario.

Utility of BCG Vaccination:

Scientists have found that heterologous protection conferred by the BCG vaccine could also be effective in patients who have contracted the COVID-19 infection. This is evident from the fact that higher mortality rates are observed in those regions not having universal BCG vaccination policies like Italy, the USA, etc. The protection that the BCG vaccine is conferring can be due to its non-specific mode of action. This means that molecular similarity between BCG and other viral antigens could have led to the formation of some memory B and T cells which can recognize both BCG and other respiratory pathogens. It has been also investigated that BCG could have stimulated the epigenetic reprogramming of the innate immune cells. The monocytes may have undergone modification at the promoter sites of the genes encoding inflammatory cytokines which are now resulting in a more active immune response as those modified monocytes have been reactivated & triggered by the coronavirus antigen in those who have received the BCG vaccination previously.

Applicability & future of Nanotechnology:

Today nanotechnology or the science of nanoscale structures is one of the most interesting branches of science. A new nanomedicine developed at the SN Bose National Centre for Basic Sciences (SNBNCBS) in Kolkata, has the potential in the treatment of Covid-19. Our body continuously adds and removes oxygen through oxidation and reduction (redox) reactions. However, reactive oxygen species (ROS) free radicals are also generated from these processes. During the viral or bacterial attack, ROS, or oxygen stress level of our body is naturally generated by our immune cells so that they can efficiently perform their functions. In the new nanomedicine formulation, nanoparticles extracted from manganese salt are combined with the citrus extract. Clinical trials on mice have shown that the new nanomedicine adds up the oxidative stress in a controlled manner and thus finds a potential application in controlling virus infections like the Covid-19. Another interesting application of nanomedicine is the use of silver nanoparticles. Colloidal silver or a suspension of microscopic, electrically charged particles of silver bear a wide potential to act against almost 650 different kinds of pathogens which include bacteria, fungus, and viruses. They aid in inhibiting the oxygen metabolizing enzymes in these pathogens. Covid-19 infections start mildly in the upper respiratory airways. Hence it can be applied through inhalation delivery methods to suppress the proliferation of the virus during the early days of infection.

Remarkable potential of CRISPR-based diagnostics & therapeutics:

CRISPR (clustered regularly interspaced short palindromic repeats) is referred to as a family of DNA sequences that are exclusively found within the genetic makeup of prokaryotic organisms. These sequences are derived from DNA fragments of some previously attacking bacteriophages. The CRISPR sequences whenever they encounters any complementary DNA sequence concerning it, they bind to that and the Cas9 (CRISPR-associated protein 9) nuclease-type enzyme associates with the CRISPR sequences & cleaves those specific strands of DNA. Thus, whenever, any future invasion of the same bacteriophage occurs, this phenomenon inactivates the invading DNA of the attacking bacteriophage thus conferring the prokaryotes with a mode of acquired immunity. This technique can be harnessed and applied in viral and pathogen rapid diagnostic and therapeutic purposes. Cas13 nuclease-type enzymes are RNA-targeting proteins by virtue of which property, these nucleases can degrade specific target RNAs without producing any effect to the host genome. This property makes Cas13 nucleases an interesting candidate for study. On the other hand, Cas12 type nucleases work on DNA. Both Cas12 and Cas13 nucleases can also cleave other nucleic acid molecules (except the target ones) present in the vicinity of their target site. This trait (called the trans or collateral cutting activity) can be applied to CRISPR diagnostics where the non-targeted nucleic acids can be utilized to make certain color-tagged probes for detection purposes.

Feng Zhang’s group first reported a CRISPR-based nucleic acid detection technique called SHERLOCK (Specific High sensitivity Enzymatic Reporter unLOCKing). Zhang and his team identified two genes (S gene and Orf1ab) from the SARS-CoV-2 genome as their targets. In the SHERLOCK protocol for coronavirus detection, firstly, the synthetic viral RNA is amplified by applying the recombinase polymerase amplification (RPA) technology. This process is followed by in vitro transcription where the amplified DNA gets converted to RNA. Then, RNA detection is done using Cas13 nuclease and specific crRNA (gRNA) targeting specific sequences. Finally, the visual color readout is done where the cleaved reporter RNA with labeled ends are captured on specific antibody bands (to form the visual test band) on lateral flow strips. This protocol has been demonstrated to detect coronavirus RNA from patient samples in very less time (almost less than an hour) and here no special instrumentation is required (as isothermal signal amplification process proceeds through a constant temperature thus not requiring the thermocycler as required by the qRT-PCR technique).

Mammoth Biosciences proposed a new method which is DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR) assay which recruits Cas12a for sensitive DNA detection purposes. The method utilizes the same CRISPR-based detection of the two genes (N-gene and E-gene) which, by bioinformatics computational methods, are found to be conserved in SARS-CoV-2 genome. This method utilized the technique of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) for amplifying the RNA strands to generate a huge number of DNA strand loops and this method takes about 30 minutes which is less when compared to the SHERLOCK-based protocol. This is because here, no extra time is required to be spent on the additional IVT steps. Such a rapid diagnostic platform would be particularly valuable in high-risk areas such as airports, clinics, and hospitals.

Other than detecting, a new CRISPR-based antiviral strategy targeting the SARS-CoV-2 virus appears to effectively degrade RNA (as has been proposed in a Stanford paper). This aids in killing or knocking out the virus which can thus be subsequently applied to the therapeutic sector. This approach, termed PAC-MAN (Prophylactic Antiviral CRISPR in huMAN cells), employs six CRISPR RNAs that can target 91 percent of the 3,051 sequenced coronaviruses, thus signifying its broad coverage. This CRISPR-based approach recruits Cas13d type RNA endonuclease which employs customizable CRISPR-associated RNAs. The reason for choosing Cas13d over other Cas13 proteins is because it has a small size, is highly specific in action, and possesses a strong catalytic activity. Cas13d is made to target & destroy two conserved sites of the SARS-CoV-2 viral genome, which encode the RdRP and Nucleocapsid proteins, known to be essential for coronavirus replication and function. This technique now needs to be tested & validated with live SARS-CoV-2 viruses and whether they are having any off-target side effects must be thoroughly evaluated via clinical screening. An effective and safe in vivo delivery method into the human respiratory tract cells must be developed. The remarkably great potential of the CRISPR-based therapeutic systems lies in the fact that once the genetic targets of a new virus are identified, altering a previous treatment becomes simple which can be quickly implemented during the birth of any future pandemics.

Conclusion:

Hence, it can be inferred from the above discussion that the BCG vaccination strategy, the application of nanomedicines, and the CRISPR-based diagnostic & therapeutic systems hold a great promise & a bright future to emerge out victoriously against the threat of Covid-19.

References

Broughton, J.P., Deng, X., Yu, G. et al.CRISPR–Cas12-based detection of SARS-CoV-2. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0513-4
Redelman-Sidi, G. Could BCG be used to protect against COVID-19?. Nat Rev Urol(2020). https://doi.org/10.1038/s41585-020-0325-9