A GENOMIC PERSPECTIVE

Bats being the natural reservoir of SARS like viruses [1], an intermediate host causes the spillover in humans. For the SARS outbreak in 2002, civets played this role [2]. Through phylogenetic analyses, coronaviruses in reservoir species are expected to be the common ancestor of the ones in intermediate hosts and infected humans. Although pangolins were speculated to be the villain for COVID-19 transmission in humans, the RBD (receptor binding domain; binds to ACE2/ ACE2 like receptor of the host species) of pangolin CoVs is less similar (91.02%) to RBD of SARS-CoV-2 at whole genome level when compared to RaTG13, the bat CoV (96.2%), deviating from the speculation [3]. Till now no intermediate host has been confirmed for COVID-19 spillover in humans. When looked at neutral mutations (mutations that are neither detrimental nor beneficial; they accumulate in absolute timescale and works as ‘molecular clocks’ to be used in phylogeny analysis), there was 83% similarity between RaTG13 & SARS-CoV-2 suggesting that the divergence is more than estimated through whole genome analysis [4]. Thus, the natural reservoir species of COVID-19 is yet to be confirmed as well.

Andersen, Kristian G., et al. (2020) have discussed three potential theories regarding the cross-species transmission of SARS-CoV-2 [5]. The first theory is about the homology between ACE2 and ACE2-like receptors in humans & the intermediate host, respectively. This feature might be exploited by fast adapting SARS-CoV-2 to evolve their RBD in the intermediates to facilitate jumping in Homo sapiens followed by a zoonotic contact.

The interaction between the key amino acids of RBD and ACE2 indicated that, other than pangolins, three different species of turtles and snakes might act as the potential intermediate hosts transmitting SARS‐CoV‐2 to humans [6]. It is also possible that via zoonotic transfer, a progenitor of SARS-CoV-2 has been transmitted in human populations where it underwent natural selection to evolve to its current highly contagious form. It is the second theory which needs strong evidence. Phylogenetic analyses revealed that 2019-nCoV arises from the predecessor strains of SARS-CoVs through recombination [7].

The third theory is focused on the worldwide speculation of this pandemic being a planned one. Is SARS- CoV-2 a synthetic construct evolved in laboratories or has it escaped the research laboratories working on Coronaviruses? However, if COVID-19 were indeed a result of artificial selection, a progenitor virus genetic background would have been required to perform manipulations. This hypothesis can be checked by tracking back the database available on Coronaviridae. Needless to say, bioinformatics experts are yet to find one and it is advisable to refrain from spreading rumors unless there is scientific basis for it.

NOTE: Refer to COVID 19 Etiology article in CONOCIMIENTO, ISSUE 1 for more details.

THE IMMUNE SYSTEM

One of the major issues of concern is the evasion of highly evolved vertebrate immune system by SARS-CoV-2. The pathogen always ends up having an upper hand in the ‘arms race’ due to its faster adaptability and high mutation rate. A brief outlook of the host pathogen co-evolution at the mechanistic level will help to develop a better understanding.

Prevalence and large genetic diversity of existing coronaviruses, their close proximity, frequent recombination and mutations produce new strains of viruses with altered host range and pathogenicity that enhance their fitness by selecting them naturally to survive in a new host. The immunity of the host starts adapting against the virus leading to reduced pathogenicity upon future infection. Seven human coronaviruses (Homo sapiens is the natural host), discovered so far, thus affect us very mildly as our immune system is well adapted against them [8]. However, when SARS-CoV-2 entered humans, the severity of the disease was significantly higher because of the start of a new round of adaptation in a new host where the innate immunity fails to eliminate the novel virus to prevent infection.

Recognition of PAMP (pathogen associated molecular patterns) by PRR (pattern recognition receptor) of the host initiates the innate immune response. After crossing the first line of defense, when the virus enters the host system, there is secretion of interferons (antiviral chemicals) and accumulation of macrophages (for phagocytosis of infected cells) at the site of infection. A complex cascade of signaling mechanisms is initiated by type I Interferon within immune cells. Natural Killer cells (NK cells) are also activated by interferons to kill the virally infected cells [9].

Through co-evolution with their hosts, viruses have developed a variety of immune escape and control mechanisms. In addition to these, many strategies are used to neutralize the cellular and humoral immune responses. Chen, Xiaojuan, et al. (2014) described how autophagy (self-destruction of the damaged or infected cells by phagocytosis), a host immune response, is being exploited by Coronaviridae. PLP2-TM, a coronavirus membrane associated protease induces incomplete autophagy by blocking the fusion of autophagosomes (key cellular structure in autophagy) with lysosomes (cell organelle with hydrolytic enzymes). Furthermore, PLP2-TM interacts with a factor Beclin1, which in turn promotes STING, the key repressive regulator for antiviral IFN signaling. These two pathways facilitate coronavirus replication and attenuate antiviral innate immunity in humans [10].

Moreover, higher mutation rate in RNA virus (10-6-10-4 substitution per nucleotide per infected cell) compared to that of DNA virus (10-8-10-6 s/nt/c) makes it change its genetic background much more frequently [11]. This feature in flu virus is the main reason, why vaccine development is still in progress, as there is high probability that the virion particle is entering the host with different attributes each time. Even the host cannot utilize the immune memory to elevate adaptive immunity responses if the virion changes drastically during future encounters. Needless to say, if SARS-CoV-2 follows this strategy, it will lead to an uncertain future. Although COVID-19 has an inbuilt 3’-5’ exoribonuclease proofreading machinery, their evolution of neutral mutation is not significantly different from other RNA viruses, suggesting lower mutagenesis to be compensated by higher rate of replication [12].

NOTE: Refer to The Warfare series of articles of CONOCIMIENTO, ISSUE 2 for more details.

AN ARMS RACE

Seemingly, COVID-19 has adapted another evolutionarily stable strategy of having less morbidity and being highly contagious. Reproductive number (R0) for SARS-CoV-2 is currently 3.28 (ranges from 1.4 to 3.9) [13]. When compared with two previous non-human CoV outbreaks, for first 1000 people to infect MERS took 903 days, SARS-CoV took 130 days & SARS-CoV-2 took 48 days. But MERS killed 34 people; SARS-CoV killed 10 people, and COVID-19 killed 2 people out of every 100 infected ones (WHO official website). Viruses are obligatory cellular parasites, developing with their hosts since the dawn of life. Being highly contagious makes a virus obtain large number of hosts and being less morbid helps to maintain itself in the host population.

No vaccines for SARS and MERS were prepared, but the pandemic stopped as it did not spread much and killed a greater number of hosts via infection. However, this theory has several flaws and needs more justification. MERS started in Saudi Arabia, 19th among the 22 countries with least population density in 2010 (https://www.worldometers.info/world-population/saudiarabia-population/). This might be the reason for a lower spread of MERS. Although there is ongoing debate on effect of heat on CoVs, high temperatures prevalent in the middle east might also hinder the spreading of MERS. However, SARS started in Wuhan just like COVID-19, but managed to infect only 8,098 people worldwide. Maybe the cases imported from foreign countries were well controlled 20 years ago. On the contrary, tighter binding of the S (spike) protein of SARS-CoV-2 to human cells[14] and its higher replication rate might explain the rapid formation of chain of infection. Tang, Xiaolu, et al. (2020) found two variants of 2019-nCoV by genetic analysis. The most contagious one (‘L’ type) is currently declining in frequency due to selection pressure by human intervention, whereas, the less aggressive ‘S’ type is getting prevalent in the population [4].

We must take a serious note about the fact that novel pathogens are residing in wildlife and such widespread epidemics may follow in coming days. Devastating rates of deforestation, urbanization and animal trafficking are increasing the contact of human society & wildlife. Are we suitably prepared enough to curb the evolutionary advantage of the pathogens? The question still remains.

REFERENCES

1. Li, W., Shi, Z., Yu, M., Ren, W., Smith, C., Epstein, J. H., & Zhang, J. (2005). Bats are natural reservoirs of SARS-like coronaviruses. Science, 310(5748), 676-679.
2. Song, H. D., Tu, C. C., Zhang, G. W., Wang, S. Y., Zheng, K., Lei, L. C., & Zheng, H. J. (2005). Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proceedings of the National Academy of Sciences, 102(7), 2430-2435.
3. Zhang, T., Wu, Q., & Zhang, Z. (2020). Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Current Biology. 4. Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., & Cui, J. (2020). On the origin and continuing evolution of SARS-CoV-2. National Science Review.
5. Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020).The proximal origin of SARS-CoV-2. Nature medicine, 1-3.
6. Liu, Z., Xiao, X., Wei, X., Li, J., Yang, J., Tan, H., & Liu, L. (2020). Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2. Journal of medical virology.
7. Kumar, S., Maurya, V. K., Prasad, A. K., Bhatt, M. L., & Saxena, S. K. (2020). Structural, glycosylation and antigenic variation between 2019 novel coronavirus (2019-nCoV) and SARS coronavirus (SARS-CoV). Virus Disease, 1-9.
8. Sloots, T. P., McErlean, P., Speicher, D. J., Arden, K. E., Nissen, M. D., & Mackay, I. M. (2006). Evidence of human coronavirus HKU1 and human bocavirus in Australian children. Journal of clinical virology, 35(1), 99-102.
9. Owen, J. A., Punt, J., Stranford, S. A., Jones, P. P., & Kuby, J. (2013). Kuby immunology. New York: W.H. Freeman.
10. Chen, X., Wang, K., Xing, Y., Tu, J., Yang, X., Zhao, Q., & Chen, Z. (2014). Coronavirus membrane-associated papain- like proteases induce autophagy through interacting with Beclin1 to negatively regulate antiviral innate immunity. Protein & cell, 5(12), 912-927.
11. Peck, K. M., & Lauring, A. S. (2018). Complexities of viral mutation rates. Journal of virology, 92(14), e01031-17.
12. Zhang, Y. Z., & Holmes, E. C. (2020). A genomic perspective on the origin and emergence of sars-cov-2. Cell.
13. Liu, Y., Gayle, A. A., Wilder-Smith, A., & Rocklöv, J. (2020). The reproductive number of COVID-19 is higher compared to SARS coronavirus. Journal of travel medicine.
14. Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367(6483), 1260-1263.

With the huge burden of increasing infections with every passing hour, the question that keeps resonating is what the origin of the SARS-CoV-2 virus is. Probably, prevention, vaccination and therapeutics would have been slightly ahead if the answer to this question was known.