Seeing the target of vaccines with your eyes - Capturing highest resolution image of a virus (Zika virus)

Hi, I am Virus, Zika Virus! Given how lethal and yet how facinating they are, if viruses had a swag it won't be any less than that of James Bond. But as science and technology spreads it wings, some day we would counter all the infectious diseases known to mankind. Nice dream, but meanwhile there is a publication taking us, not much, but maybe one step closer.

Your friend Zika virus just uploaded its picture

An image depecting structure of Zika virus. This resolution is less than image in current study.
Source: https://commons.m.wikimedia.org/ Created by user Starless on https://rcsb.org/structure/5IRE
License: CC0

Legend of Viruses and vaccines - the war of the molecules
Viruses are these tiny buggers (just few nanometer in size) and rendering millions of humans life, as lifeless as themselves. They are mostly just a piece of genetic material (DNA or RNA) wrapped inside a protein coat called caspid and sometimes an extra lipid membrane , with envelope proteins. While one way to make vaccines against the virus is to either use non virulent attenuated or a deactivated virus, we still don't have vaccines for all of them. However finding and making a non virulent strain may not always be practical. Moreover when we use whole deactivated viruses we can't control to which part of the virus the immune system will build immunity against. (If you are wondering how many parts can this 20 nanometer thing can have , wait till you see the picture). Now that viruses are fast mutating son of bitches it may render the vaccine worthless faster than we can think of a new course of action. To our rescue comes the technology of using only particular subunits of viruses, which we know are unique in sequence and structure and change the least among different mutated strains. Given this people use all kind of techniques to visulaize the structure of these buggers, so we can find a solution to known infectious diseases. Moreover knowing the structure not only help you to pick the part of the virus to be used for vaccine , but it also gives you power to now design drugs against it computationally.

A breif history of Zika virus - I mean it, really brief
One such bugger that we are going to see today is called Zika virus. For starters it belongs to the family of Dengue virus and West Nile virus(Musso et al., 2016), yes the same ones that cause hemolytic fevers. Though Zika was thought to be benign a few years ago, more evidence of its role in different human pathology is now emerging. It has been shown to cause congenital defects such as, microcephaly (small head) in new borns if the mother was infected. It also is a trigger of Guillain-Barré syndrome(Plourde et al,2016), the one which your own immune system turns against your neurons. In a nutshell it looks like Zika doesn't like humans to have neurons for whatsoever reason. And we don't like it for that.

The Zika virus is a single stranded RNA virus. That is to say that it's genetic material is RNA, which it injected into cells if your body to make copies of itself. This genetic material is packed inside a icosahedral enveloped coat. For all I care the virus can be a hyperdimensional cube, but it is sequence and structure of these proteins of the surface is what matters which matters. It is what you want to see, know and play around with if you want to build drugs and vaccines against it. It's like seeing you in skin if I want to know what are unique marks, patters, or textures on you as compared to other humans.

Seeing the skin of a virus

To see something as small as a virus, more importantly the molecular structure of its surface, you just can't use a light microscope. Initially, a lot of molecular structures have been deciphered by X-ray crystallography and NMR including that of many viruses. However it's a long process to crystallize virus particles, that is if you succeed to crystallize it. An easier way is to instead use an electron microscope to look at them. It's not like people have not imaged a virus before under an electron microscope before. In fact recently Passos et al., 2017 imaged HIV virus with resolution of 6 Armstrong or 6*10^-10 m (a single atom is somewhere about 1 A). When the Zika virus became a pain in the ass a couple of years ago they used CryoEM to image it as well(Sirohi et al.,2016). But these guys achieved a new feat in this study(seveanna et al., 2018). They used better sample prep and optimised their algorithm and took an Image at resolution of 3.1 Armstrong (resolution is quality of image indicating the mininmum distance between two points that is clearly visible. So smaller this distance is the more details you can see).

So how do they do it and what information did they gain?

The trick this paper used to achieve this goal was single particle Cryo electron microscopy. Well for Noobs, electron microscopy is a technique in which you use a beam of electrons instead of light to see stuff. Since resolution is limited by wavelength of beam the electron beam overcomes this by having a very small wavelength and hence more resolution. Cryo means that the sample is prepared and imaged at around -196 degree C. At this temperature one you do need to modify your sample with all the chemical procedure required for convention electron microscopy. Plus CryoEM provides a higher resolution images than conventional EM. (I remember to do cryoSEM of collagen in tissue, all I ever had to do was freeze the tissue in liq N2 and crack it open on the CryoSEM stage). Well, as if killing these two birds with one arrow is not enough, the single particle Cryo EM further increases the resolution by a computational algorithm. That is, it takes 1000s of images of identical particles and then use statistics to build the 3D structure of the particle. (Ofcourse that might make some people frown because it is not an image created by beam but by algorithm. To me it seems to work nonetheless). So essentially the paper is all about optimising this data processing algorithm to arrive at such high resolution. If you see their figure 1 you can now yourself see the neat high res image.

You may ask, so what? Another virus seen at yet higher resolution. Does this study does anything beyond that. As it so happens the authors further compared the Zika virus with other viruses of the same family, such as dengue and West Nile viruses. They not only pinpointed the structures unique to Zika but they also pinpointed potential drug binding sites on the surface of the virus. See figures 4 and 5 in the paper

**Read more about - **
Viruses types and their classifications
https://www.ncbi.nlm.nih.gov/books/NBK8174/
Zika Virus
www.who.int/news-room/fact-sheets/detail/zika-virus
Single particle Cryo Electron microscopy
https://www.cell.com/cell/fulltext/S0092-8674(15)00370-0

References
Musso D, Gubler DJ. 2016. Zika virus. Clin Microbiol Rev 29:487–524. doi:10.1128/CMR.00072-15.

Plourde AR, Bloch EM. A literature review of Zika virus. Emerg Infect Dis. 2016 Jul [date cited]. http://dx.doi.org/10.3201/eid2207.151990

Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N,
Kvaratskhelia M, Craigie R, Lyumkis D. Cryo-EM structures and atomic model of the
HIV-1 strand transfer complex intasome. Science. 2017 Jan 6;355(6320):89-92. doi:
10.1126/science.aah5163. PubMed PMID: 28059769; PubMed Central PMCID: PMC5508583.

Sirohi D, Chen Z, Sun L, Klose T, Pierson TC, Rossmann MG, Kuhn RJ. The 3.8 Å
resolution cryo-EM structure of Zika virus. Science. 2016 Apr
22;352(6284):467-70. doi: 10.1126/science.aaf5316. Epub 2016 Mar 31. PubMed PMID:
27033547; PubMed Central PMCID: PMC4845755.

Sevvana M, Long F, Miller AS, Klose T, Buda G, Sun L, Kuhn RJ, Rossmann MG.
Refinement and Analysis of the Mature Zika Virus Cryo-EM Structure at 3.1 Å
Resolution. Structure. 2018 May 29. pii: S0969-2126(18)30170-9. doi:
10.1016/j.str.2018.05.006. [Epub ahead of print] PubMed PMID: 29958768.