COVID-19 origin conundrum

Along with a viral outbreak, many conspiracy theories emerge-it is unavoidable. Conspiracy theories flourish and spread even more virally than the viral disease. More interestingly, such conspiracy thinking may not disappear even after the outbreak subsides. If you look at the history of AIDS, vaccines, or any novel therapeutic interventions in the past, you may find several such theories which are still floating around. It is human tendency to easily distrust other groups, which may be the heart of conspiracy thinking. My efforts here is to present what the Science says so far about the origin (keep in mind, this is an area where serious investigations are happening now- our views may change accordingly). We are seeing thousands of deaths daily, crippled economy and health system throughout the world by this tiny string of RNA coated in a lipid layer. We need to dig into the available Scientific data to develop an opinion about the origin of this virus. Researchers are working round the clock to solve many questions with regard to the nature of this virus, the features of the disease, cure for COVID19 and revealing more about this virus every day.

With regard to the Origin of SARS CoV2, there are three main possible scenarios, 

a) Bioengineered origin– this virus is designed, cloned and prepared by molecular virologists somewhere in a secret lab and deliberately released to a population (as bioweapon) to eradicate the human race? (this virus is not selective for a specific regional population).

b) Natural origin– this virus, is natural origin and got transmitted to humans from wildlife (a zoonotic transfer happened from a bat or through an intermediate host).

c) Accidental lab-escape– this virus got leaked from a lab conducting research on bat Coronaviruses. Either through improper disposal of viral samples or through researcher accidentally got infected and became the patient zero for this worldwide mess.

Origin: Bioengineered or Natural?

I would take the two scenarios a) Bioengineered origin and b) Natural origin together since they are addressing same kind of question. To know more about a virus, uncovering its genomic sequence is very essential.

SARS CoV2 sequence in public database

In December 2019, an outbreak of acute respiratory syndrome was first reported in humans (Wuhan, China). The exact date of the first report is still under investigation and being updated according to the evolving events- so far, we know that the first hospitalized case was on December 12th. According to WHO, they were informed about the cases of pneumonia on December 31st, 2019. Initially it was thought human to human transmission may not occur. While on 24th January 2020, in scientific journal Lancet published a study from China on familial cluster of pneumonia suggesting the person-to-person transmission. It is quite impressive that after the first report the genomic sequence of SARS CoV2 was published within weeks by a team lead by Chinese researchers and deposited in GenBank open access public database on first week of January. They published their work in in scientific journal Nature, where they submitted their data to that journal on January 7th 2020.

One of the main criticisms was the delay in the publishing SARS CoV2 sequence. Noticing that first report was on December 12th, publishing sequence in public database within weeks’ time is impressive. Naming a disease and knowing this vital sequence information helped us all around the world to understand more about the causative agent of this disease, to create tests and to design vaccines. Thanks to the modern technology, it took several months after the first report to release the sequence of past outbreak SARS-1 (2002-2003).

Bat coronavirus research labs under suspicion

Though several viral labs have the capability to do world class research on viruses, due to its location at the epicenter of COVID-19 outbreak (Wuhan) and the presence of a bat coronavirus lab, Wuhan virology Institute (WIV) came under suspicion. Prof. Shi Zhengli in Wuhan Institute of Virology (WIV) is a renowned bat Corona virologist, known as the ´bat woman´ in the field. She is well known in the scientific world for her extensive contributions in understanding the SARS coronaviruses. Once applauded as hero, now fiercely criticized by the conspiracy theorists around the world for her research on bat coronaviruses. Let’s dig into the relevant works from Prof. Shi Zhengli and her collaborators.

Shi Zhengli´s research lab in Wuhan Institute of Virology (WIV) also sequenced this virus and published in scientific journal Nature on 3-February-2020. This scientific article provided vital information regarding the contagion. They found that, this virus belongs to SARS family (before that it was an ´unknown ´disease in Wuhan), they also sequenced this novel virus (which helped to design the test for detecting the virus), the entry mechanism of this virus into the host cell (cell surface protein ACE2 receptor helps the virus to provide the entrance). They took the samples from the patients and analysed complete genetic sequence (RNA) of this virus. They noticed that novel Corona virus is 96% identical to a bat coronavirus (bat CoV RaTG13). Thevirus shared 79.6% sequence identity to SARS-CoV (the lab was conducting researches on both viruses). From an evolutionary point of view this 96% similarity is not very close (note we share nearly 96% genomic similarity with our cousin chimpanzee). According to Prof. Edward Holmes (whose was in a different team that sequenced SARS CoV2) points out that the sequence divergence (is equivalent to almost 20-50 years apart). Considering the slow pace at which this virus is mutating, it may take several years for those bat viruses from WIV to attain the present form, as SARS CoV2.

She was in the scientific team that found the connection between the bat and the SARS CoV1 outbreak in 2002 and warned such spillovers from natural bat reservoir may happen in future also. Her team found the ´origin´ cave (Yunnan, China) and a population of bats (smoking gun) from which 2002 SARS Coronavirus might have jumped and ultimately reached humans through civet cats as intermediate hosts (2002-2003 SARS killed nearly 800 people). They predicted the possibility of similar spillovers from bat to humans or through an intermediate host in future.

She was also involved in a controversial study on a chimeric coronavirus (word chimera is from Greek mythology; a creature with lion´s head, goat´s body and dragon´s tail).  The chimeric virus was made with bits and pieces from different viruses, and the study was designed and conducted by US lab (Dr. Vineet Menachery and team at Prof. Ralph Baric´s lab in University of North Carolina), in which Prof. Shi Zhengli was a collborator. They created a lab-engineered virus with SARS backbone with a spike protein from a horseshoe bat coronavirus (SHC014). Contrary to predictions from sequences, their experiments proved that the spike protein in chimera can bind to ACE2 receptor of host cells and is vital for infecting and grow in mice and human airway cells in petri dishes (caused illness in mice). This controversial but crucial study showed that SHC014 virus can infect human cells and could be a potential threat for future outbreak. What was the rationale for making a chimeric virus? They claimed, such a chimeric virus-based approach may help us to find the potential pre-pandemic viruses. This designed/engineered virus got fierce criticisms from some members of scientific community.

Recently, Prof. Ralph Baric´s lab proposed the possibility of using stable, engineered SARS CoV as replacement of live-attenuated virus vaccine. Live-attenuated virus vaccine is a savior and used successfully for fighting against deadly diseases like polio, measles, mumps, chickenpox etc, but poses a risk of reverting back to virulent form by mutation or recombination events (rare chances though). Baric´s lab deleted the gene tools from the SARS viral genome that help the virus to recombine, thereby handicapped it from reverting back to its virulent form. Their strategy is advantageous to create attenuated vaccine for CoVs in general, as several zoonotic CoV outbreaks are happening recently (several outbreaks even before COVID19).

The above mentioned are the most relevant scientific research articles from Shi Zhengli and her US collaborators that links them to coronavirus. None of these labs under suspicion were doing any secret researches. While, they were publishing their research works in several journals in the past as well as during this present outbreak. In fact, their research helped us to understand more about the SARS CoV in general otherwise it would have been difficult to fight against this virus even to this extent. Dr. Peter Daszak (a member of the team that found the link between bat and SARS) says ´´she should be lauded as hero, not vilified”. 

´Errors make us to evolve´- Mutations lead to natural evolution

Mutations are the keys for evolution, this happens in all species. Viruses produces numerous progenies harbouring mutations that too very fast, we are experiencing evolution in front of us. Such mutations accumulate during viral propagations which sometimes may result is a new strain with significant genetic drift from an ancestor virus (see the diagram below).

Several random copying errors occur during replications of genetic material of SARS CoV2 inside a host cell, the reason why there are many mutations during transmissions. SARS CoV-2 is the largest RNA virus known, with nearly 30,000 bases giving more chances for copying errors. In general, RNA dependent RNA polymerase (RdRp); the protein machine that makes copies of RNA does not have efficient proofreading mechanism like our DNA coping system. Such viruses ´always´ mutate and accumulate mutations during the process of transmission from one infected individual to another. Due to frequent mutations, viruses that causes flu escapes our immune surveillance system and that is the reason why every year we need different flu vaccine. Very interestingly, RdRp of SARS CoV2 has a proof-reading mechanism (if error happens while copying, a part of machine will correct it). Hence experts predict that it may take several years to see a major genetic/antigenic drift when compared to a flu virus which is a fragmented RNA virus. Compared to flu virus the ´copier machine´ for SARS CoV2 is less error prone, and the genetic material is a single RNA-string hence natural immunity that survivors attain by infection may defend us for longer time period (though predictions on a novel virus is complicated). These copying errors made by the virus (that makes a new strain) are useful for researchers to trace the tracks of the viral propagation which is very important during an epidemic episode to understand more about the route-map of pathogen.

Reports on SARS CoV2 mutations

A natural mutant of SARS CoV1 was reported recently, where a 29-nucleotides deletion happened in its genome during its early transmission, that made it less virulent. Sometimes a deletion of a large chunk from the genome may result inactivation of essential genes (change in a couple of alphabets (nucleotides) may not affect a virus, but several changes may change the nature of the virus). The gene that was affected by this deletion is called ORF-8 (a gene supposed to help in replication of this virus). More interestingly a deletion of 382-nucleotide deletion was already noticed from Singapore in a BioRxiv manuscript (whether this strain of virus is the reason for the relatively less damage caused by COVID-19 in Singapore, will be interesting to study). 

SARS CoV2 sequence comparisons

Comparison of the published genomic sequence of SARS CoV2 with that of the other viruses will help us to identify where this virus belongs to. Several scientific articles came out suggested the high sequence similarity of SARS CoV-2 with bat CoVs (RatG13), proposing the possibility that this CoV may be transmitted from bat mostly through an intermediate host. Their data supported the possibility that SARS CoV-2 is a natural mutant and debunked the ´designed/engineered virus´ hypothesis. One research group compared sequences of an important part of the key viral protein (spike) and noticed that it matches with that of the pangolin CoV. The reason pangolins as the intermediate host thus came into picture. Also, SARS CoV2 virus optimized itself during initial propagation (possibly in intermediate host) by acquiring furin cleavage site in on the spike protein, that helps in fine tuning the host range. This virus is notorious for stealing genetic materials from similar CoV from the host (the mechanism is called recombination), and current thinking is that the ancestor SARS CoV from a bat from China leaked into intermediate host and acquired some gene sequences by recombination event from host CoV, before jumping into humans as SARS CoV2 causing this outbreak (see the diagram below). Note, millions of inefficient viruses fail during these processes, while a very few viruses become successful in adapting to new host. 

Early spillover?

It should be perceived very clearly that we noticed COVID19 by the end of 2019. That does not necessarily mean that this virus jumped from bats towards the end of 2019, it only means we detected it then. It is difficult to predict how long we had this virus among our population. SARS CoV2 might have infected the ´patient zero´ several months or even years before we detected it. Prof. Robert Garry proposes (article in journal Nature medicine) such a scenario that the virus might have spilled into human population long back and was silently optimizing itself to its present form (check interesting history of origin of AIDS pandemic). Virus adapts to a new species by undergoing mutations and sometimes recombination while propagating. On this road, the chances for a novel virus to fail is high. Hence, both natural events like recombination as well as genomic mutations helped in the making of this ´perfect virus´ named SARS CoV2.

Lets come to another pandemic, AIDS and tracing the history of HIV origin. We came to know about this virus HIV and the deadly disease AIDS in 1981, but analyses of older blood samples and genetic sequences of HIV changed our views about the origin of AIDS. Current understanding is human population was having HIV infections long back even first decades of 19th century. The spillover might have happened from monkeys to a bush-hunter in Congo, Africa around 1920s. Similarly, a retrograde analysis of the patient samples stored from hospitals may change the history of COVID19 too (it is tough when compared to HIV, to retrogradely analyse the long history of this virus since SARS CoVs don’t integrate into host genome like HIV). Isolating viral genomes from already collected patient samples (with regard to other ailments with similar symptoms) and analyses may give some insights into COVID19 history.

Zoonotic diseases

SARS and MERS were also originated from bats through civet cats and camels as intermediate hosts respectively. In the recent past, Ebola was reported first from African continent, MERS from Middle East, Nipah outbreaks were reported from Malaysia and later from Indian subcontinent. HIV is another zoonotic disease that spilled over from monkeys, in beginning of 19th century. Nature carries out high-throughput mutation experiments on these viruses (mainly by copying errors and by recombination) in different species.When other animals including us come in close contact with such nature´s viral reactors, some of the mutated viruses may find a new host causing serious illness. Such zoonotic diseases (diseases that are transmitted from animals to humans) will happen in future also. Moreover, we already know about hundreds of different viruses from bats, and thousands of unknown viruses are waiting in bat reservoirs that may pose future outbreaks (works from Dr. Peter Daszak).

Nature has several high-throughput viral labs

Nowadays, we have the technology to manipulate the viral genome by introducing specific mutations in genomes and make engineered viruses for research purposes (to understand the basics of viruses and preparing preventive & curative measures in case of potential outbreaks). But our technology is very modest so far, compared to nature´s massive approach. Though we have the ´know-how´, so far in most of the cases it is hard, and the functional prediction of engineered mutations may not be very accurate. One has to screen a ton of mutants to pick up the right one (remembering Yogi Berra, ´´in theory there is no difference between theory and practice; in practice there is´´). 

Just after the SARS CoV2 sequence in public domain, a non-peer reviewed manuscript appeared (later disappeared) in BioRxiv that claimed sequence similarity between regions of SARS CoV2 and HIV. Recently, Luc Montagnier (2008 Nobel prize winner in medicine and physiology, for his discovery of HIV) argued that SARS-CoV2 contains some genes of HIV hence could be an engineered one. It is easier to find some degree of similarity in bits and pieces of genetic sequences between any 2 species (if you check for sequences of two different types of viruses you may find some similarities in a certain parts of their genetic sequence), which is not a big deal since most of these similar sequences may not be functionally relevant. Further, in case a deliberate genetic manipulation was performed (designed or engineered virus) it is easy to identify ´the genetic markers´ on such reverse genetic backbone of coronavirus genomes. A group of expert scientists all over the world carefully analyzed the sequence of SARS CoV2 and published their verdict in scientific journal Lancet, that this virus is of wildlife origin.

Based on several research articles from multiple labs around the world on SARS CoV2, a) the designed/engineered SARS CoV2 virus theory can be debunked. There is strong consensus among the experts in the field on b) the wildlife origin of this virus (they made several collective statements and reviews in scientific journals with regard to its natural origin).

Accidental release from a high safety viral lab?

Now the question remains whether this virus was leaked out from a bat coronavirus research lab. Accidental releases of smallpox and anthrax samples (though inactive) from high containment lab were reported in the past from US facilities. Intriguingly, Virology institute in Wuhan (WIV) at the epicenter of this outbreak has bat coronavirus research lab, which led to the speculation of a possible lab-escape from their facility. Also, several ´patient zero´ (the first patient or the carrier of an infectious disease) stories were circulating in media and one among them is, a researcher from WIV as the patient zero. For a novel infectious disease, it may take months to years to find the patient zero. We may not even find that patient, especially this disease with enormous asymptomatic transmission. Chinese authorities stated that none of the employees associated with WIV were known to be infected. Currently we don’t have any evidences to prove that a leak happened from a high-safety lab and that caused this pandemic (we may know the truth one day, but takes time). Based on the data so far, the genetic sequence of the bat coronavirus on which the WIV lab was working does not show similarity with that of SARS CoV2 (RatG13 Vs SARS CoV2). Concerns were raised by leaders of many countries on this issue and investigations are being done currently. WHO recently expressed its interest to work with investigations by Chinese government on the origin of this novel coronavirus.

BSL4 lab-Safety first

Coming to the level-4 lab in Wuhan Institute of Virology (WIV), it is a modern facility completed in 2015 (first in the Chinese mainland), in collaboration with French Institute CIRI (a total cost was 44 million USD). WIV has many international collaborations and publishes frequently in top scientific journals about their research suggesting transparency (WIV is a pioneer on bat coronavirus research). 

Research on microbes are usually conducted under very strict guidelines all over the world (to avoid any accidental release into nature from the lab). A biosafety level (BSL) facility is an enclosed laboratory facility, with very strict set of biocontainment regulations (the facility deals with dangerous biological agents). The levels of biocontainment range from the lowest biosafety level 1 (BSL-1) to the highest at level 4 (BSL-4). There are less than 50 BSL-4 facilities around the world. BSL-4 is the highest level of biocontainment and is highly expensive to create one and to maintain it. Such labs are often very controversial. In a BSL-4 lab, the operating rules are extreme (it should be). Access is very limited, change of clothing before entering the facility, should use positive pressure suits, shower on exit and use of filtered air are some of the requirements. Decontamination of all wastes before removal from facility (please watch the video links attached on routines in a BSL-4 facility). Chances are very rare for a biological agent to escape from such a high containment facility.

To conclude

There is no doubt about the wildlife origin of SARS CoV2. With the genomic sequence analyses, it is assumed that the spillover happened from a bat to human, possibly through an intermediate host. During early propagations before jumping into humans, it got optimized and made a ´perfect human virus´ that led to this pandemic. The probabilities are high that SARS CoV2 spilled from a wild creature to humans (based on previous SARS1 and MERS spillovers) from the Wuhan wet market. Accidental release from a high biocontainment lab is in general a rare possibility. The genome sequence of SARS CoV2 is not similar to the bat coronaviruses in WIV. Further investigations are warranted to find out whether there was any accidental leakage of an ancestral virus from the BSL-4 facility from WIV lab, to disprove the ´lab-escape´ hypothesis. It is interesting to see what new evidences that the US President have regarding his claims that COVID19 originated from Wuhan lab. This disease became a crisis for humanity now, it’s time to help each other to fight against this invisible enemy.

Even if there are plenty of evidences to substantiate the natural origin and transmission of this virus, those evidences may never satisfy conspiracy thinkers. Please don´t glance through the media headlines and conclude, in most cases the sensational headlines do not reflect the contents. Read through it and check the evidences they present to support their claims. Soon, we may hear other conspiracy theories like COVID19 is a pharma-conspiracy, or there is no SARS CoV2 virus (virus deniers, there are HIV deniers), or ´alien origin´ of this virus (why not, why should there be a limit for imagination?). Psychology behind, adhering to conspiracy theories will be a very interesting area to study. One may cling hard illogically to his/her favorite conspiracy theory; despite how much scientific evidences you display in front. Perhaps, blindly believing such conspiracies is easier than spending time and energy to understand the facts.

Videos of this blog

Biosafety level lab routines 

References

The proximal Origin of SARS CoV2

https://www.nature.com/articles/s41591-020-0820-9

SARS CoV1

https://science.sciencemag.org/content/310/5748/676

Chimpanzee and Human genome

https://www.nature.com/articles/nature04072

Prof. Shi Zhengli´s work

https://www.nature.com/articles/s41586-020-2012-7

https://www.nature.com/articles/nm.3985

https://www.nature.com/articles/nature12711

https://www.nature.com/articles/s41586-020-2012-7

Prof. Ralph Baric´s work

https://www.nature.com/articles/nm.3985

https://www.nature.com/articles/s42003-018-0175-7

Other labs on Origin of SARS CoV2

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30251-8/fulltext

https://onlinelibrary.wiley.com/doi/full/10.1002/jmv.25688

https://www.sciencedirect.com/science/article/pii/S1567134820300447?via%3Dihub

Pangolin Origin

https://www.sciencedirect.com/science/article/pii/S0960982220303602

SARS CoV-2 and HIV (BioRxiv)

http://dx.doi.org/10.1101/2020.01.30.927871

Lancet; statement of experts

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30418-9/fulltext

WHO guidelines for BSL-4

Accidental release of anthrax and smallpox samples

https://www.bbc.com/news/world-us-canada-28221185

https://www.bbc.com/news/world-us-canada-32910020

China lab WIV

https://www.nature.com/news/inside-the-chinese-lab-poised-to-study-world-s-most-dangerous-pathogens-1.21487

https://time.com/5824061/wuhan-lab-denies-link-coronavirus-outbreak/

SARS CoV-2 sequence publishing

https://www.sciencemag.org/news/2020/01/chinese-researchers-reveal-draft-genome-virus-implicated-wuhan-pneumonia-outbreak

https://www.ncbi.nlm.nih.gov/nuccore/MN908947

https://www.nature.com/articles/s41586-020-2008-3

https://www.sciencedirect.com/science/article/pii/S0092867420303287?via%3Dihub

Familial cluster in China (first report)

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30154-9/fulltext

29 nucleotide deletion of SARs CoV1 (2002-2003)

https://www.nature.com/articles/s41598-018-33487-8

Recombination of SARS CoV2

https://www.biorxiv.org/content/10.1101/2020.02.10.942748v2

382-nt deletion of SARS CoV2

https://www.biorxiv.org/content/10.1101/2020.03.11.987222v1

Published by Rajeev

Neuroscientist, living in the North, passionate about brain, new molecular tools, viral vectors.

2 thoughts on “COVID-19 origin conundrum

  1. Very well explained differentiation between the lab theory and direct market infection possibility. I’m still very interested in knowing what would be the outcome after the investigation happens( if it happens) 🙂

    Like

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