Youtube Instagram
Science Corner

ATTACK ON THE VIRUS

By: Adhella Menur

On November 5, 2023, the final episode of an epic anime called “Attack on Titan” (AoT) was aired, leaving the fans with vague feelings. At first, the dark fantasy written by Hajime Isayama was expected to be a cliche storyline centered on a boy heroine who wants to defeat gigantic man-eating humanoids referred to as Titans. However, the story progressed with intensive twists, deep-dive characterization, and roller-coaster emotions. Throughout the 89 episodes, fans were questioning: who the real monster is, what is humanity, and why wars will not end after all attempts. Isayama was not hesitant to bring out “The Rumbling,” when millions of Colossal Titans swept through 80% of human population. Even though the global alliance successfully stopped The Rumbling and ended the Titan power, the peace was not eternal. In the post-credit scene, the cycle of violence inevitably resumes, and another war erupts even without the Titan existence.

In our real world, after more than three years of battle with the SARS-CoV-2 that killed more than 6.9 million people, humanity, represented by the WHO, declared victory and ended the global emergency status for COVID-19 on May 5, 2023. The WHO Director-General warned that the virus is still killing and changing. The risk remains of new variants emerging that cause new surges in cases and deaths. The attack on the virus was as epic as the attack on Titan. Lessons learned should be attained as much as possible to prepare for future threats.

The origin of Titan vs. the virus

In the AoT anime, the writer decided to make an ancient species of aquatic worm from the Cambrian period (500 million years ago), Hallucigenia, nicknamed “spinal worm,” responsible for forming Titan power. The first human who transformed into Titan was initially infected with the Hallucige-nia. While fans are satisfied with the complete explanation of the Titan’s origin, humanity is still uncertain about the origin of the SARS-CoV-2 infection. Two major theories have been long debated: a natural spillover through zoonosis followed by sustained human-to-human spread or introduction of a virus into humans from a laboratory source.

Coronaviruses are widely present in the animal world; in humans, seven pathogenic coronaviruses have been identified in the last 20 years. Most human coronaviruses (HCoVs) are zoonotic in origin, and their evolution is linked to a high level of urbanization and animal breeding, which facilitates the exchange of species and simplifies the crossing of species barriers and genomic reorganization. After many years of surveying wild animals, researchers concluded that bats serve as the main reservoir for the virus and need intermediate hosts, where the virus acquires some or all the mutations necessary for efficient human transmission. Two previous dangerous HCoVs, SARS-CoV and MERS-CoV, had confirmed this spillover event. For SARS-CoV origin, a series of investigations found that the virus existed in masked civet cats and raccoon dogs that bats infected. Antibodies to the virus in a badger were later found at a Chinese live animal market in Shenzhen and were suspected to be the source of the human infection. For MERS-CoV origin, researchers found that dromedary camels were an essential reservoir for MERS-CoV originating from bats and predicted interspecies transmission occurred more than 30 years ago. Additionally, dromedary camels in Saudi Arabia have been found to have multiple MERS-CoV genetic lineages, involving crossing various barriers and causing outbreaks in humans.

Figure 1. (A) The origin of Titan, an infection of powerful Hallucigenia.
(B) Zoonotic origin theory of SARS-CoV-2 with circumferential evidences found in the Huanan market (Worobey M, et al., doi: 10.1126/science.abp8715). Created with Biorender.com

The remaining mystery in the SARS-CoV-2 origin – spillover theory – is what animal serves as the intermediate host. The Huanan Market in Wuhan, China, was identified as a likely source of the spill-over event, where wild live SARS-CoV-2–susceptible animals, such as palm civets, mink, rac-coon dogs, hog badgers, red foxes, and pangolins, were sold. Spatial analyses within the market reported that SARS–CoV–2–positive environmental samples, including cages, carts, and freezers, were associated with activities concentrated in the southwest corner of the market where vendors sell wild animals. Moreover, in the early SARS-CoV-2 infections, the virus was classified into two line ages, A and B; lineage B emerged before lineage A and had a direct epidemiological link to the market. Early lineage A isolates were not directly linked to the market but were isolated in patients who resided within 2.31 km of the market. Lineage A was later isolated from an environmental sample in the market. Multiple spillover events might have occurred between late October and mid-November 2019 rather than a single spillover event at one point. However, an analysis of animals at the market during the outbreak did not identify a single species as the intermediate host. Therefore, everything is still circumferential pieces of evidence. The second theory, laboratory-related theory, was more attractive to many people. The Wuhan Insti-tute of Virology (WIV)—a laboratory where scien-tists study coronaviruses—is in the same city. Scientists in WIV were intensively studying SARS-related viruses after the 2002–2003 SARS-CoV global spread. They were working on CoV diagnostics, isolation of CoV and vaccine development in high biosafety standards (BSL3 or 4) and pos-sessed many collections of SARS-CoV samples from bats. People assumed the outbreak resulted from a lab leak of manipulating coronaviruses and a previously infected lab staff member bringing the virus to the market. Additionally, in May 2021, the US President asked intelligence agencies to probe the virus’s origins, but they could not reach a consensus. Some agencies even shifted from a neutral stance on the virus’ origin to one favoring, with “low confidence,” a lab leak. However, the WHO investigation team produced a 150-page report from the fact-finding mission that said the outbreak was unlikely to be a lab accident. Scientists in WIV also have a routine health surveillance program, and a study showed that no SARS-CoV-2 positive in lab staff despite extensive epidemiologic tracing of early cases.

Alwine JC et al., in “A Critical Analysis of the Evidence for the SARS-CoV-2 Origin Hypotheses”, beautifully explained how the lab-related theory was unlikely. The virulence of SARS-CoV-2 depends not only on the furin cleavage site but also on the cleavage site loop length; this knowledge was not attained before 2020; deliberate engineering of the SARS-CoV-2 cleavage site without this critical information is improbable. Also, there is a signature of laboratory handling in SARS-CoV-2: the loss of the furin cleavage site in the spike protein during cell culture – however, early isolates of SARS-CoV-2 showed the furin cleavage site to be intact, arguing against the introduction into hu-mans after laboratory cell culture. To simplify, it is too complicated for scientists to make a compatible virus such as SARS-CoV-2. The authors remind us that scientific conclusions are based on likelihood given the scientific data, and findings can change as new data are obtained. For now, the available evidence favors the zoonotic theory. Nonetheless, the virus’s origin may remain a mystery for humanity, but open a wide range of research to prevent the event from happening again.

Figure 2. SARS-CoV-2 has revealed a complex relationship between the presence of a furin cleavage site and viral attachment, which the lab technology before 2020 still lacked knowledge of (figure from Brown EF, et al, https://doi.org/ 10.3390/cells11111801). Created with Biorender.com.

The variants and recombinants

In the AoT anime, Titans have many variants, from the mindless Pure Titans to the more sophisticated Titan shifters. Pure Titans are the weakest and most generic Titans whose behavior is easy to predict, making them easy to kill. Abnormal Titans are Pure Titans with unusual behavior and intelligence, allowing them to perform unpredictable moves. The Nine Titans, also known as Titan Shifters (Attack, Colossal, Armored, Female, Beast, Jaw, Cart, War Hammer, and Founding), are the strongest; each can shift back and forth between human and Titan form to access their Titan’s abilities. SARS-CoV-2 also has many variants due to its consistent mutation throughout the pandemic. A variant is a viral genome (genetic code) that may contain one or more mutations. Mutations are prone in all RNA viruses in each cycle of replication. Even though SARS-CoV-2 has a proofreading enzyme that allows high-fidelity replication to maintain the integrity of a long viral RNA genome and limit the error rate imposed by viral RNA polymerases, mutations still occur due to how efficient the virus is. At first, the evolution rate was observed to be approximately two mutations per month. However, abundant mutations emerged, particularly in the Spike protein, implying that the evolution rate is higher than predicted.

The WHO is tracking all SARS-COV-2 variants, and some are identified as variants of concern (VOC) due to their significant impact on public health (increased transmissibility and virulence, more severe disease, or immune escape), such as Alpha, Beta, Gamma, Delta, and Omicron. Some are labeled as variants of interest (VOI) and under monitoring (VUM). Alpha (B.1.1.7) was the first of the highly publicized VOC. Alpha first appeared in Great Britain in November 2020 with key spike mutations: N501Y, H69/V70, P681H, and Y144. Beta (B.1.351) was identified in South Africa at the end of 2020 with key spike mutations: N501Y, E484K, K417N, L18F, D80A, D215G, and A701V. Gamma (P.1) was first found in Brazil in January 2021 with key spike mutations: K417T, E484K, and N501Y. Then, those VOCs faded away with the rise of the more aggressive Delta variant. Delta (B.1.617.2) was first identified in India in late 2020 with key spike mutations: R158G, L452R, T478K, D614G, P681R, and D950N. Delta variant was the worst nightmare over the course of the pandemic because it is highly transmissible, replicating more efficiently, attacking lungs frequently, and causing severe disease, especially in unvaccinated persons. The Delta variant was swept away by Omicron (B.1.1.529), first identified in Botswana and South Africa in late November 2021. Initially, Omicron was so worrisome due to its tremendous mutations and really distinct from previous variants. Over 60 mutations were identified, consisting of substitutions, insertions, and deletions, of which over half were accumulated in the spike (key: D69–70 deletion, T95I, G142D/ D143–145 deletion, K417N, T478K, N501Y, N655Y, N679K, and P681H). Luckily, up to now, Omicron has not been acting like Delta. Even though it has higher transmissibility and immune escape, the case fatalities were reduced compared to Delta, which may be attributed to the lack of the TMPRSS2 pathway that did not let it habitat lungs.

Figure 3. Size comparison of some Titan shifter variants to human to the virus. Upper: phylogeny of SARS-CoV-2 variants from the beginning of the pandemic to August 2023 (Nextstrain.org). Created with Biorender.com.

Multiple subvariants of Omicron have been identified, and new ones continue to emerge. The original version of Omicron is no longer circulating. More than 300 Pango lineages are currently associated with the Omicron variant; some have an unofficial media nickname. The ‘standard’ subvariant is now referred to as BA.1 (or B.1.1.529.1), and the two other subvariants are known as BA.2 (or B.1.1.529.2) and BA.3 (or B.1.1.529.3). In mid-2022, BA.4 (or B.1.1.529.4) and BA.5 (or B.1.1.529.5) were detected in several countries. Moreover, some Omicron subvariants were recombinants, resulting from genomes of two variants or subvariants combined during viral replication, for example, XBB, a recombinant of the BA.2.10.1 and BA.2.75 subline-age. After the Delta variant wave, we observed several case surges that were still manageable or mini waves caused by the Omicron subvariants. At the end of 2023, the descendant of BA.2.86 caused the latest mini wave: JN.1 (BA.2.86.1.1). JN.1 was first detected in the United States in September 2023. It continues to be reported in multiple countries, and its prevalence has rapidly increased globally. Due to its rapidly increasing spread, the WHO has classified JN.1 as a VOI since December 19, 2023. It contains more than 30 mutations in the spike, making it highly capable of evading the pre-existing anti-SARS-CoV-2 immunity. The JN.1 has a hallmark mutation L455S in the spike and three other mutations in the non-spike. Currently, there is no evidence that JN.1 presents an increased threat to public health compared to different circulating variants. However, it is still can cause fatal cases, particularly in elderly and immunocompromised patients. There is one certainty that it will not be the last virus attack. Something new will emerge if there is a virus mini-wave somewhere in the world.

The Survey Corps Titan research – The Scien-tists

In the AoT anime, a branch of Military division called the Survey Corps had a crucial role in the story. The Survey Corps was most actively involved in direct Titan combat, Titan research, human expansion, and world exploration. They hoped that someday, their efforts would change the world, and they would be able to recover what had been taken away from humanity. The character that resembled an energetic and quirky scientist was named Hange Zoe. Hange initially had a very hateful heart towards Titans, which killed many of Hange’s comrades, but when Hange kicked the head of a 3-meter Titan, Hange was shocked at how abnormally light it was. This droves Hange to take an extreme and outside-the-box approach to Titan research. Hange even kept some Titans alive for the sake of experimentation to better understand the nature of these beats and their weaknesses. Upon learning that there was a power to transform into a Titan, research was conducted to uncover the extent of Titan shifter abilities. This would grant the Survey Corps vital information when dealing with enemies with this power. Hange also led the engineering team to invent new weapons, such as the Titan guillotine and the thunder spear, that effectively killed Titans.

Figure 4. Clinical management of COVID-19 according to scientific evidence throughout the pandemic (figure from Zhu Y, et al, doi: 10.3389/fimmu.2023.1116131).

It is such a familiar story regarding the attack on the virus. Borrowing the concluding remarks of Alwine JC et al.: “Science was our best ally during the pandemic, working to understand virus replication, spread, and disease to produce life-saving vaccines, antivirals, rapid tests, and treatments.” The more we curious and understand our enemies, the more effective our approach to defeat them and prevent future threats. Such groundbreaking scientific discoveries have never been so swiftly and efficiently applied in human history.

One of the precious scientific breakthroughs is the mRNA vaccine, which produces robust immune responses against SARS-CoV-2 spike RBDs, preventing the viral spread and limiting the disease severity. The 2023 Nobel Prize in Physiology or Medicine has been awarded to a pair of scientists, Professors Katalin Kariko and Drew Weissman, who developed the technology that led to the mRNA COVID-19 vaccines. Karikó and Weissman showed in the early 2000s that it was possible to dampen the body’s inflammatory responses to lab-made mRNAs by making specific chemical changes to the component bases of the molecules—findings that allowed future groups to deliver genetic instruction into human cells to make viral proteins and lead the body to produce immunity. Quickly developing a vaccination against nearly any disease is the central tenet of the technology – as long as you know the correct genetic instructions. This allows for considerably faster and more flexible vaccine development compared to traditional methods.

Attack on the virus: season finale or to be continued to a new season?

Can we confidently say goodbye to the COVID-19 pandemic? After the WHO ended the global health emergency status, countries shifted to handling the virus as an endemic pathogen. As they want to catch up with the economy, many countries let down their guard, dismantle the systems it has built, and send the message that COVID-19 is now nothing to worry about. Observing this trend, even the PLOS Neglected Tropical Disease (NTD) Journal now invites the community of NTD scientists to submit COVID-19 papers. Markov PV et al. stated that the best-case scenario for the future evolution of SARS-CoV-2 whereby there will be continued antigenic drift within the Omicron lineage, such that over short and medium timescales, immunity elicited by a combination of vaccination and prior infection protects against severe disease on reinfection and provides broad immune responses that will cover considerable continued evolution of the virus. The worst-case scenario is that antigenic evolution would be disrupted by the emergence of a new variant with an entirely different constellation of mutations and phenotypic properties, which will allow the virus to evade immunity established by prior infection or vaccines. Several hypotheses explain the emergence of VOC: sustained stealth circulation of SARS-CoV-2 in humans in areas with poor genomic surveillance, zoonotic circulation of SARS-CoV-2 in animal reservoirs (risk of spillover and spillback events), and chronic SARS-CoV-2 infections in immunocompromised individuals. As the immunity from previous infections and vaccines wane over time, unclear government policies, discontinuing research due to limited support, public ignorance, and vaccine inequality may lead to the worst scenario (hopefully not!).

As WHO’s technical lead, Maria Van Kerkhove, said, “We can’t forget the graves that were dug” – we should not forget how many frontliners died, saving lives during the pandemic. Like the Survey Corps in the AoT anime screamed, “Shinzou wo sasageyo!” – “Dedicate your heart!”; to win the battle, we should deliver our best as individuals for our community. Start to take care of our health, apply standard health precautions to prevent transmission, take vaccine or booster if available, follow reliable reports, spread awareness, and keep fighting. Anyway, happy new year 2024! May the year bring health, many joys, and more achievements!

Source of Inspiration

Leave A Comment

Your Comment
All comments are held for moderation.

Related Posts