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SARS-CoV-2

SARS-CoV-2 – The vaccine landscape

11 March 2020 by Vincent Racaniello

by Helen Stillwell

Helen is a research associate in David Hafler’s immunobiology lab at Yale University; previously, she worked on poxviruses at Tonix Pharmaceuticals, and she plans to apply to PhD programs in virology this year.

Is there a vaccine for SARS-CoV-2? The internet is awash with articles and posts seeking to shed light on this very question.

Currently, there is no approved vaccine against SARS-CoV-2. While several companies have announced vaccine candidates in development, it is still unlikely that a vaccine will play a significant role in the current outbreak.

In the US, vaccine candidates cannot proceed through the appropriate preclinical, clinical, regulatory, and manufacturing pipelines in a mere few weeks. Typically, under non-outbreak circumstances, vaccine development can cost up to $1 billion or more, and it often takes many years to reach approval (Dunn 2020). That being said, certain allowances can be made in the case of an outbreak, and we are getting better at developing platform technologies that allow for the development of viable candidates at increasingly faster rates.

Globally, the therapeutic pipeline for SARS-CoV-2 contains about 15 potential vaccine candidates (Pang et al. 2020). These candidates employ various different technologies, including messenger RNA (mRNA), DNA-based, nanoparticles, synthetic and modified virus-like particles (Pang et al. 2020).

The two principal candidates are those being developed by Inovio Pharmaceuticals and Moderna Therapeutics (in partnership with the NIAID). Both vaccines rely on specific mechanisms that fall under the umbrella term “platform technologies”. That is, both vaccines consist of a primary nucleic construct (in this case RNA or DNA) that is amenable to the insertion of pertinent genetic sequences from a virus of interest so that the construct can be adapted for use against various different viruses. They are ‘platforms’ that allow for more efficient development of vaccine candidates against emerging viruses, such as SARS-CoV-2.

Both candidates are partially funded by the Coalition for Epidemic Preparedness Innovations (CEPI), a global partnership between public, private, philanthropic, and civil society organizations that possesses the resources to fast-track the development of vaccines against emerging infectious disease and enable access to these vaccines during outbreaks. While it will likely take a year or more for the majority of the vaccine candidates to initiate Phase I clinical trials, those funded by CEPI are able to accelerate these timelines (Pang et al. 2020).

The Inovio vaccine is a DNA-based vaccine (Pang et al. 2020). It is in the preclinical stage of development, and phase I testing is projected to occur in the next few months (Pang et al. 2020). Phase I clinical trials for vaccines typically include 20-100 healthy volunteers who are administered a vaccine candidate for the purpose of evaluating safety and determining ideal dose.

The Moderna-NIAID vaccine is a mRNA vaccine. Typically, mRNA vaccines include an open reading frame (ORF) for the target antigen and are flanked by untranslated regions (UTRs) with a terminal poly(A) tail (Zhang et al. 2019). Theoretically, after vaccine delivery, mRNA vaccines are translated to drive transient expression of antigen to promote an immune response (Zhang et al. 2019).

Recently, Moderna escalated development and sent vaccine to NIAID to begin the process of initiating a phase I trial to test the safety and immunogenicity of the vaccine. The trial is projected to begin at the end of April, with preliminary results in July or August (Loftus 2020). The time it took Moderna to develop and prepare the vaccine after learning of the virus’ genetic sequence from Chinese scientists in January is extraordinary. Following the outbreak of SARS-CoV in China in 2002, it took approximately 20 months for NIAID to get a vaccine into the first stage of human testing, according to NIAID Director Dr. Anthony Fauci (Loftus 2020).

Yet, it is still unclear whether Moderna’s vaccine candidate will provoke a sufficient immune response to be effective against SARS-CoV-2. The premise of gene-based platform technologies rests on the ability to target segments of the viral genome that are involved in provoking host immune response. Although we can make well-informed choices on what sequences provoke immunogenicity, we won’t know if the optimal sequence has been selected until human trials are completed (Loftus 2020). So too, there is no precedence for a vaccine of this kind since there are not yet any approved human vaccines that use this gene-based technology (Loftus 2020).

Virologist Dr. Jose Esparza commented the following on Moderna’s vaccine candidate: “The rapid manufacturing of the RNA vaccine is great. But preclinical experiments are important to assess safety before carefully moving ahead with small phase I trials in human volunteers. Special attention should be placed to a potential ‘Antibody Dependent Enhancement of Infectivity’ triggered by the induction of binding but no neutralizing antibodies.”

Indeed, the fast development of a vaccine and imminent phase I testing do not guarantee its efficacy. We will not know until after human trials whether the sequence Moderna and NIAID selected provokes a sufficient immune response to impart protection. And, even if the first studies show encouraging results, the vaccine might not be widely available until 2021 due to the later phase clinical trials and regulatory supervision that will be required to allow for its use in the general public.

To date, the best source of protection against SARS-CoV-2 remains to be the recommendations of the CDC and similar organizations: avoid close contact with those who are sick; avoid touching your eyes, nose and mouth; remain home when you are sick; cover your cough or sneeze with a tissue and discard properly; clean and disinfect frequently touched surfaces; wear a facemask if you are showing symptoms (face masks are not beneficial to those who are well).

References

Dunn A. The Wuhan coronavirus has now claimed more lives than SARS. Top scientists told us it could take years and cost $1 billion to make a vaccine to fight the epidemic. Business Insider. (2020). https://www.businessinsider.com/wuhan-coronavirus-vaccine-could-take-years-timeline-and-cost-2020-2.

Loftus P. Drugmaker Moderna Delivers First Experimental Coronavirus Vaccine for Human Testing. Wall Street Journal. (2020). https://www.wsj.com/articles/drugmaker-moderna-delivers-first-coronavirus-vaccine-for-human-testing-11582579099.

Pang J, Wang MX, Ang IYH, Tan, SHX, Lewis RF, Chen, JI, Gutierrez RA, Gwee SXW, Chua PEY, Yan Q, Ng XY, Yap RKS, Tan HY, Teo YY, Tan CC, Cook AR, Yap JCH, Hsu LY. Potential Rapid Diagnostics, Vaccine Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review. J. Clin. Med. (2020) 9(3). doi: 10.3390/jcm9030623.

Zhang C, Maruggi G, Shan H, Li J. Advances in mRNA Vaccines for Infectious Diseases. Front. Immunol. (2019). doi: 10.3389/fimmu.2019.00594

Filed Under: Basic virology, Helen Stilwell Tagged With: COVID-19, SARS-CoV-2, vaccine, viral, virology, virus, viruses

TWiV 590: COVID-19 and coronavirus – we have mail

8 March 2020 by Vincent Racaniello

The TWiV trio continues in-depth coverage of COVID-19 and SARS-CoV-2, including discussion on genome mutation and circulating lineages, handwashing, facemasks, cruise ship outbreaks, the South Korean situation, and much more.

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Show notes at microbe.tv/twiv

Filed Under: This Week in Virology Tagged With: antiviral, coronavirus, CoV, COVID-19, cruise ship, genome mutation, pneumonia, SARS-CoV-2, vaccine, viral, virology, virus, viruses, Wuhan

SARS-CoV-2 coronavirus case fatality ratio

5 March 2020 by Vincent Racaniello

Driving the anxiety and uncertainty about the current outbreak of COVID-19 is the case fatality ratio (CFR) being thrown about carelessly by not just the press, but also WHO and other organizations. However the CFR is not a one-size-fits all, and is influenced by many factors.

[Read more…] about SARS-CoV-2 coronavirus case fatality ratio

Filed Under: Basic virology, Commentary, Information Tagged With: case fatality ratio, CFR, COVID-19, SARS-CoV-2, viral, virology, virus, viruses

SARS-CoV-2: Could it be bad?

27 February 2020 by Vincent Racaniello

coronavirusHealth experts say it’s not a question of whether SARS-CoV-2 will spread within the U.S., but when. A CDC official said yesterday, “We are asking the American public to prepare for the expectation that this might be bad.” What exactly does that mean?

[Read more…] about SARS-CoV-2: Could it be bad?

Filed Under: Basic virology, Commentary, Information Tagged With: case fatality ratio, coronavirus, COVID-19, epidemic, pandemic, SARS-CoV-2, viral, virology, virus, viruses, Wuhan

TWiV 588: Coronavirus update – Save the pangolin!

23 February 2020 by Vincent Racaniello

The TWiV team returns this week to SARS-CoV-2019 coverage to review the latest epi curves, the fatality rate, furin cleavage site and receptor binding domain in the spike glycoprotein, related CoV recovered from pangolins, evidence that the virus did not escape from a laboratory, and many more questions sent in by listeners.

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Filed Under: This Week in Virology Tagged With: ACE2, China, coronavirus, CoV, COVID-19, epidemic, evolution, furin, pangolin, pneumonia, receptor binding domain, respiratory aerosol, SARS-CoV-2, spike glycoprotein, viral, virology, virus, viruses, Wuhan, zoonosis

Pangolins and the origin of SARS-CoV-2 coronavirus

20 February 2020 by Vincent Racaniello

coronavirus SpikeA coronavirus related to SARS-CoV-2 has been isolated from Malayan pangolins illegally imported into Guangdong province. It is not the precursor of SARS-CoV-2, but comparison of viral genome sequences provides further evidence that the virus currently infecting humans was not produced in a laboratory.

There are two important sequences in the viral spike glycoprotein (pictured) that are important for tracing the origin of SARS-CoV-2: a furin cleavage site (discussed last week) and the receptor binding domain (RBD).

The results of experiments in cells in culture have shown that the SARS-CoV-2 spike glycoprotein binds the cell receptor ACE2. Six amino acids in the RBD are critical for binding to this receptor. Five of these six amino acids differ in the RBD of SARS-CoV-2 compared with sequence from the bat virus RaTG13, the most closely related virus. The SARS-CoV-2 spike glycoprotein binds ACE2 with high affinity, an outcome not predicted by computational analysis of the RBD sequence. If someone were to engineer an RBD into a bat SARS-like CoV to allow efficient infection of human cells, they would not use the amino acid sequence in the SARS-CoV-2 spike. Rather the specific sequence was likely selected during replication in cells with human-like ACE2.

As discussed previously, the furin cleavage site in the SARS-CoV-2 spike is not present in the bat virus RaTG13. Its acquisition could allow enhanced infection of human cells. In addition to the furin cleavage site, an extra proline is also present, a change predicted to lead to the addition of O-linked glycans in the vicinity. If someone were to engineer the furin cleavage site into the spike, it is not likely that the extra proline would have been included. Furthermore, the addition of such glycans typically occurs under immune selection.

The genome sequences of CoVs recently isolated from pangolins are not close enough to SARS-CoV-2 to have been its immediate progenitor. However, the RBD of these pangolin CoVs are identical to that of SARS-CoV-2 at 6 of 6 of the key amino acids discussed above. This observation indicates that passage of CoV in a host with human-like ACE2 could select for a RBD with high-affinity binding. Such passage could also select for insertion of the furin cleavage site, which is not present in pangolin CoVs. Once a virus with the appropriate RBD and furin cleavage site arose in an animal – a bat or intermediate host – it would then replicate once introduced into humans.

Another possibility is that viruses with the correct RBD have been repeatedly jumping into humans, but efficient human to human transmission was not established until the acquisition of the furin cleavage site. Such is the scenario with MERS-CoV, which has jumped multiple times from camels to humans, but each chain of infection is short and soon ends. The virus has never become established in humans because the required mutations have not entered the viral genome. Serological surveys specific for SARS-CoV-2 might test this hypothesis for its emergence.

Could laboratory passage of a bat SARS-like virus lead to isolation and accidental emergence of SARS-CoV-2? This scenario would require starting with a virus that is very close to the current isolates. Passage in cell culture might have selected for the RBD amino acid changes to enable high affinity ACE2 binding. However this virus would have had to be very similar to SARS-CoV-2, and no such isolate is known to be present in any laboratory. Selection of viruses with a furin cleavage site would likely have taken extensive passaging in cells. Finally, it is unlikely that the O-linked glycan addition site would have emerged without immune pressure, which is absent in cell cultures.

Proving or disproving any of these hypotheses for the emergence of SARS-CoV-2 might never be possible. Nevertheless, isolation of SARS-like viruses from a variety of animals might help to clarify the steps to emergence in humans. For MERS-CoV, a priority should be to prevent human infections, perhaps by immunizing camels, to avoid the emergence of another epidemic CoV with sustained transmission in humans.

Filed Under: Basic virology, Information Tagged With: ACE2, coronavirus, COVID-19, furin, O-glycan, pangolin, receptor, receptor binding domain, SARS-CoV-2, spike glycoprotein, viral, virology, virus, viruses

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