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COVID-19: size, real image

COVID-19: size, real image


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I'm an electronics engineer. I was thinking about how to detect the presence of COVID-19:

  1. Obtain the sample.

  2. Increment image/sample, (I need the real size to determine increment/magnification)

  3. Digital image processing - detect presence using artificial intelligence or Recognition.

What is the approximate size of COVID-19? Is there a real image of COVID-19?


2019-nCoV also has enveloped virions that measure approximately 50-200 nm in diameter with a single positive-sense RNA genome.

  • Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study, The Lancet (2020)

The Coronavirus Unveiled

In February, as the new coronavirus swept across China and shut down entire cities, a scientist named Sai Li set out to paint its portrait.

At the time, the best pictures anyone had managed to take were low-resolution images, in which the virus looked like a barely discernible smudge.

Dr. Li, a structural biologist at Tsinghua University in Beijing, joined forces with virologists who were rearing the virus in a biosafety lab in the city of Hangzhou. Those researchers doused the viruses with chemicals to render them harmless and then sent them to Dr. Li.

Dr. Li and his colleagues then concentrated the virus-laden fluid from a quart down to a single drop. He could only hope that they had done everything just right, so that the weeks of work to produce that drop would not have been a waste.

“At the time, you don’t know what’s inside,” Dr. Li said. “It’s just liquid, right?”


In that case we will still live with COVID-19 but a modified type of it?

Personally, I think that is very likely to happen.

In that case it is likely to get more or less severe?

It is difficult to foresee. I am an HIV specialist and we have been looking at HIV for 30 or 40 years now. It is difficult to say whether it is more or less severe than it was 30 years ago. The “problem” (from an evolutionary point of view) is that we have treatment for HIV, so, very fortunately, that natural evolution no longer happens.

The same thing might happen with coronavirus: the treatment or vaccine will become available and we will never see this natural evolution. Viruses, especially of those types, tend to be very inventive and they adapt. This virus is new for the human population but is 96% identical to a virus transmitted within bats. That is very close – with HIV you have a variation of 20%, so one type of HIV can be only 80% identical to another.

Is it good or bad news for us?

This virus existed and changed at some point – that 4% of difference is important, as it means the virus started to infect people. The same happened 100 years ago with the simian immunodeficiency virus, the HIV analogue for monkeys, which jumped from monkeys to humans. Now it is a human virus.

This COVID is now a human virus too and will spread into the human population. If we do not stop it with modern technologies, like a vaccine, it will stay with humans for hundreds of years.

The US has already announced testing of a vaccine. How long should it take?

There is a lot of technology available, different platforms to use, but in the end, you cannot predict [how long it will take]. Take the story of hepatitis: in the 1980s, the first vaccine was developed for hepatitis B there is now a vaccine for hepatitis A, but hepatitis C has no vaccine. Furthermore, HIV has no vaccine – and we’ve been looking for 30 years.

The problem is, there are animal viruses related to coronaviruses (the feline enteric coronavirus, for example), where the vaccine proved to be dangerous: the vaccinated cats got an even more severe infection.

The danger is that people or companies and academics will rush into vaccine trials without taking precautions and accidents may happen. But again, we cannot predict – it could be as simple as the measles vaccine. I, along with you and everybody else on earth, do hope so.

If it appears to be as difficult as producing a vaccine for HIV, what is the most probable scenario?

Well, I am not that pessimistic I know HIV very well and I know why it is so difficult. This COVID virus is closely related to the SARS virus – up to 95% – so maybe the possibility for the virus to change (it’s “genetic space”) is not that large. Testing in vitro suggests antibodies for SARS could neutralize this virus, so maybe it will be fine maybe in half a year's time we will have a realistic perspective on a vaccine. But, as I just explained, there are risks that should be taken into account.

We will all live between hope and fear for a while. In the end, humankind will overcome this challenge too – but we will pay a price.


Author summary

Covid-19 has brought the international scientific community into the eye of a storm. Collaboration between researchers, public health workers, and politicians is essential to deal with this challenge. One of the pieces of the puzzle is analysis of epidemiological trends so that both the current and immediate future situation can be carefully evaluated. For this reason we have employed a daily generic growing function to describe the cumulative cases of Covid-19 in several countries and regions around the world, and particularly the European countries during the Covid-19 outbreak. Our model is completely empirical, meaning it relies solely on the daily data update of new cases and does not require assumptions to make predictions. In this manuscript, we detail the methods employed and the degree of confidence we have obtained during this process. We obtain predictions with a success greater than 90%, which means that around 90% of the value of the reported cases are inside the prediction intervals. This can be used for other researchers collaborating with and advising health institutions around the world during the Covid-19 outbreak or any other epidemic that follows the same pattern. We hope it may help facilitate policy decisions, the review of in-place confinement measures, and the development of new protocols.

Citation: Català M, Alonso S, Alvarez-Lacalle E, López D, Cardona P-J, Prats C (2020) Empirical model for short-time prediction of COVID-19 spreading. PLoS Comput Biol 16(12): e1008431. https://doi.org/10.1371/journal.pcbi.1008431

Editor: Benjamin Muir Althouse, Institute for Disease Modeling, UNITED STATES

Received: May 8, 2020 Accepted: October 9, 2020 Published: December 9, 2020

Copyright: © 2020 Català et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: The data employed had been published daily by WHO and European Centre for Disease Prevention and Control (ECDC) and is available at https://github.com/catalamarti/Gompertz_Catala2020/blob/main/Data_ECDC.xlsx.

Funding: CP, PJC and MC received funding from La Caixa Foundation (ID 100010434), under agreement LCF/PR/GN17/50300003 PJC received funding from Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR), Grup Unitat de Tuberculosi Experimental, 2017-SGR-500 CP, DL, SA, MC received funding from Ministerio de Ciencia, Innovación y Universidades and FEDER, with the project PGC2018-095456-B-I00. This work has been also partially funded by the European Commission - Directorate-General for Communications Networks, Content and Technology through the contract LC-01485746 to CP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.


Novel Coronavirus SARS-CoV-2 Under the Microscope

The National Institute of Allergy and Infectious Diseases Rocky Mountain Laboratories (NIAID-RML), located in Hamilton, Montana was able to capture images of the novel coronavirus (SARS-CoV-2, previously known as 2019-nCoV) on its scanning electron microscope and transmission electron microscopes. SARS-CoV-2 causes COVID-19 disease which has resulted in a global pandemic.

This scanning electron microscope image shows SARS-CoV-2 emerging (the round gold objects) from the surface of cells cultured in a lab. SARS-CoV-2 is the virus that causes COVID-19. The virus shown was isolated from a patient in the United States. Credit: NIAID-RML.

This is a micrograph of SARS-CoV-2 virus particles that were isolated from a patient. The image was captured under a transmission electron microscope and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

This is a transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a patient. The image was captured using a transmission electron microscope and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

This image captured with a scanning electron microscope shows SARS-CoV-2 (the round magenta objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2 is the virus that causes COVID-19. The virus shown was isolated from a patient in the United States. Credit: NIAID-RML.

This transmission electron microscope image shows SARS-CoV-2, the virus that causes COVID-19 isolated from a patient in the United States. Virus particles are shown emerging from the surface of cells cultured in the lab. The spikes on the outer edge of the virus particles give coronaviruses their name, crown-like. Credit: NIAID-RML.

This scanning electron microscope image shows SARS-CoV-2 (in yellow), the virus that causes COVID-19 isolated from a patient in the United States, emerging from the surface of cells (blue and pink) cultured in the lab. Credit: NIAID-RML.

A transmission electron microscope was used to capture SARS-CoV-2 virus particles isolated from a patient. The image was captured and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

This scanning electron microscope image shows SARS-CoV-2 (in yellow), also known as 2019-nCoV, the virus that causes COVID-19 isolated from a patient in the United States, emerging from the surface of cells (pink) cultured in the lab. Credit: NIAID-RML.

This is a transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a patient. The image was captured and color-enhanced at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

This scanning electron microscope image shows SARS-CoV-2 (the round blue objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2 is the virus that causes COVID-19. The virus shown was isolated from a patient in the United States. Credit: NIAID-RML.

This transmission electron microscope image shows SARS-CoV-2, the virus that causes COVID-19 isolated from a patient in the United States. Virus particles are shown emerging from the surface of cells cultured in the lab. The spikes on the outer edge of the virus particles give coronaviruses their name, crown-like. Credit: NIAID-RML.

This scanning electron microscope image shows SARS-CoV-2 (in orange), the virus that causes COVID-19 isolated from a patient in the United States emerging from the surface of cells (green) cultured in the lab. Credit: NIAID-RML.

How Can I View COVID-19 Under the Microscope?

The novel Coronavirus (SARS-CoV-2) causes COVID-19 disease and can be viewed under a scanning electron microscope or a transmission electron microscope. Viruses can not be viewed under standard light compound microscopes.

What is a Scanning Electron Microscope?

A scanning electron microscope (SEM) scans a sample with a focused electron beam and acquires images with information about the samples' topography and composition. Scanning Electron Microscopes are widely used in nanotechnology, materials research, life sciences, semiconductor, raw materials and industry.

What is a Transmission Electron Microscope?

A transmission electron microscope (TEM) uses beams of electrons transmitted through a specimen to form an image. The specimen is usually an ultra-thin section less than 100nm thick. The image is magnified and focused onto an imaging device such as a layer of photographic film.

Transmission electron microscopes are capable of imaging at a significantly higher resolution than light microscopes, due to the smaller de Broglie wavelength of electrons. This allows the TEM to capture fine detail, even as small as a single column of atoms, which is thousands of times smaller than a resolvable object seen in a light microscope.

Transmission Electron Microscopes are used in cancer research, virology, materials science, nanotechnology, paleontology, and semiconductor research.

Microscope Questions?

If you have any questions regarding scanning electron microscopes, transmission electron microscopes, or simple light microscopes contact Microscope World and we will be happy to help.


Are there other ways COVID-19 could spread?

One proposed alternative route SARS-CoV-2 may take to reach a new host is fecal-oral transmission, which is thought to have played a role in the spread of SARS. In Hong Kong, for example, “there was a huge outbreak [of SARS] due to an infected individual who lived on the top of an apartment building whose sewage caused a blockage,” says Heymann. The blockage is thought to have subsequently contaminated the bathing areas of people living on the floors below, leading to many new cases.

A change in mode of transmission is a big deal for a virus. It’s a bit like growing an extra arm for us, or another eye.

Recent reports of a similar situation with COVID-19, in which people on different floors of an apartment building in Hong Kong were diagnosed with the disease, led to concerns that fecal-oral transmission might be occurring for SARS-CoV-2. A couple of studies from researchers in China also recently documented viral RNA in the feces of infected people.

On their own, these observations don’t show that COVID-19 is spread via feces. Viral RNA can often be present without the virus being infective, Heymann says.

A couple weeks ago, a few news organizations also reported concerns about vertical transmission (in which a mother passes the virus to her fetus or newborn) after a woman in Wuhan with COVID-19 gave birth to a baby who was later diagnosed with the disease. Some viruses are transmitted vertically: Zika virus, for example, can infect a fetus via the placenta, while HIV can be passed through breastmilk.

Newborns diagnosed with COVID-19 are more likely to have caught the illness through the usual means—that is, close contact and exchange of virus-carrying respiratory droplets, says Mackay. “There do seem to be fairly good indications that those infections were acquired at birth, rather than in utero, because there were infected people such as a mother or a nanny who were in close proximity.”

One recent study of nine pregnant women with COVID-19 failed to find evidence of vertical transmission. In a paper published in The Lancet, the researchers reported that, in all nine cases, amniotic fluid, cord blood, breastmilk, and the newborn babies tested negative for the virus. “Findings from this small group of cases suggest that there is currently no evidence for intrauterine infection caused by vertical transmission in women who develop COVID-19 pneumonia in late pregnancy,” the authors conclude in their paper.

Another potential mode of viral spread, airborne transmission, was discussed by a Shanghai official in early February. When airborne, infective virus can drift through the air as an aerosol. In this form of transmission, “very small droplets that come out of our mouth very quickly evaporate the water off, and we’re left with a gel kind of material . . . that forms a bit of a protective environment for those virions to survive for longer,” Mackay explains. This is distinct from droplet-based spread of the virus.

Viruses such as measles that do show airborne transmission can spread further than viruses transmitted in respiratory droplets. But Mackay says that there is no evidence to suggest that SARS-CoV-2 is spread through airborne transmission. Within 24 hours of the Shanghai official’s comments, the Chinese Center for Disease Control and Prevention had put out a statement emphasizing that there was no indication that SARS-CoV-2 is spread in this way.

It’s possible, though not very likely for the time being, that SARS-CoV-2 will adopt a new mode of transmission as it evolves, Mackay says. “A change in mode of transmission is a big deal for a virus,” he says. “It’s a bit like growing an extra arm for us, or another eye.”

Given the ease with which it’s currently spreading via respiratory droplets, he adds, “at the moment, I don’t think the virus really needs to adapt too much further to its ability to transmit from human to human. It’s doing a really good job right now.”


New Images of Novel Coronavirus SARS-CoV-2 Now Available

This scanning electron microscope image shows SARS-CoV-2 (yellow)—also known as 2019-nCoV, the virus that causes COVID-19—isolated from a patient in the U.S., emerging from the surface of cells (blue/pink) cultured in the lab.

This scanning electron microscope image shows SARS-CoV-2 (yellow)—also known as 2019-nCoV, the virus that causes COVID-19—isolated from a patient in the U.S., emerging from the surface of cells (blue/pink) cultured in the lab.

NIAID’s Rocky Mountain Laboratories (RML) in Hamilton, Montana, produced images of the novel coronavirus (SARS-CoV-2, previously known as 2019-nCoV) on its scanning and transmission electron microscopes on Tuesday, Feb. 11, 2020. SARS-CoV-2 causes COVID-19 disease, which has grown to be a global public health emergency since cases were first detected in Wuhan, China, in December 2019. RML investigator Emmie de Wit, Ph.D., provided the virus samples as part of her studies, microscopist Elizabeth Fischer produced the images, and the RML visual medical arts office digitally colorized the images.

Note that the images do not look much different from MERS-CoV (Middle East respiratory syndrome coronavirus, which emerged in 2012) or the original SARS-CoV (severe acute respiratory syndrome coronavirus, which emerged in 2002). That is not surprising: The spikes on the surface of coronaviruses give this virus family its name – corona, which is Latin for “crown,” and most any coronavirus will have a crown-like appearance.

These images are available to the public for free high-resolution download on the NIAID Flickr page. NIAID asks all who use the images to please credit NIAID-RML unless otherwise noted in the Flickr image description.


Structure of COVID-19 virus hints at key to high infection rate

A Cornell study of the structure of SARS-CoV-2, the virus that causes COVID-19, reveals a unique feature that could explain why it is so transmissible between people. The Cornell group also notes that – aside from primates – cats, ferrets and mink are the animal species apparently most susceptible to the human virus.

Gary Whittaker, professor of virology in the College of Veterinary Medicine, is senior author of “Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop,” which published April 19 in the Journal of Molecular Biology.

The study identifies a structural loop in the SARS-CoV-2 spike protein, the area of the virus that facilitates entry into a cell, and a sequence of four amino acids in this loop that is different from other known human coronaviruses in this viral lineage.

An analysis of the lineage of SARS-CoV-2 showed it shares properties of the closely related SARS-CoV-1, which first appeared in humans in 2003 and is lethal but not highly contagious, and HCoV-HKU1, a highly transmissible but relatively benign human coronavirus. SARS-CoV-2 is both highly transmissible and lethal.

“It’s got this strange combination of both properties,” Whittaker said, noting the researchers are focused on further study of this structural loop and the sequence of four amino acids. “The prediction is that that loop is very important to transmissibility or stability, or both.”

Other recent research has identified a bat in China that carried a coronavirus with a similar loop but a different sequence of amino acids, which adds another lead for future inquiry, Whittaker said.

The researchers also compared the SARS-CoV-2 structural model with those of coronaviruses found in other animals and confirmed SARS-CoV-2 originated in bats. It had been suggested that the virus may have passed through pangolins (a scaly anteater), but comparisons of viral sequences and structures found no evidence of that, according to the study.

“How [SARS-CoV-2] got into humans is still unclear,” Whittaker said.

A newly identified genetic sequence in SARS-CoV-2 points to the possibility of an unknown intermediate host, he said.

Cats, ferrets and minks are also susceptible: In order to infect a cell, features of the spike protein must bind with a receptor on the host cell’s surface, and cats have a receptor binding site that closely matches that of humans. To date, infections in cats appear to be mild and infrequent, and there is no evidence that cats can, in turn, infect humans.

Whittaker added that investigations into feline coronaviruses could provide further clues into SARS-CoV-2, and coronaviruses in general.

“We are keeping an open mind to see if similar things may happen in cats that already that are now happening in humans,” he said.

Javier James, a postdoctoral researcher in Whittaker’s lab, is the study’s first author. The work is supported by the National Institutes of Health.


Author summary

Society and the media alternate between hope and despair in response to the temporary decrease or increase of daily new COVID-19 infections. The number of cases has been dependent on the political measures that were adopted in each country. Accordingly, there is a strong demand for quantifying the effects of individual measures. The reproduction number, defined as the average number of cases directly caused by a single infected case, is one of the indices of the current infectivity status. To capture the time-varying reproduction number correctly, it is necessary to incorporate the distribution of delays, which are widely dispersed from 2 to 14 days for the case of COVID-19. We have developed a state-space method for estimating the reproduction number solely from an available dataset of the number of daily cases. Our method automatically detects the change-points in the reproduction number. We apply our method to the real data and examine if the detected changes are consistent with the times at which political measures had been taken in each country. Furthermore, our method can be used to predict the number of new cases in the future to examine the possible consequences of alternative political measures.

Citation: Koyama S, Horie T, Shinomoto S (2021) Estimating the time-varying reproduction number of COVID-19 with a state-space method. PLoS Comput Biol 17(1): e1008679. https://doi.org/10.1371/journal.pcbi.1008679

Editor: Roger Dimitri Kouyos, University of Zurich, SWITZERLAND

Received: August 21, 2020 Accepted: January 6, 2021 Published: January 29, 2021

Copyright: © 2021 Koyama et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: The application program and example datasets are available at our website https://s-shinomoto.com/COVID/ and the site hosted publicly on GitHub, accessible via https://github.com/shigerushinomoto.

Funding: This work has been funded by New Energy and Industrial Technology Development Organization (NEDO) (to SS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.


Molecular Architecture of the SARS-CoV-2 Virus

SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, the detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in pre- and postfusion conformations were determined to average resolutions of 8.7-11 Å. Compositions of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed overall processing states of the native glycans highly similar to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNPs) and their higher-order assemblies were revealed. Overall, these characterizations revealed the architecture of the SARS-CoV-2 virus in exceptional detail and shed light on how the virus packs its ∼30-kb-long single-segmented RNA in the ∼80-nm-diameter lumen.

Keywords: SARS-CoV-2 coronavirus cryo-EM cryo-electron tomography ribonucleoprotein spike glycoprotein subtomogram averaging virus assembly virus structure.


Difference between COVID-19 & Flu

Influenza (Flu) and COVID-19 are both contagious respiratory illnesses, but they are caused by different viruses. COVID-19 is caused by infection with a new coronavirus (called SARS-CoV-2), and flu is caused by infection with influenza viruses.

COVID-19 seems to spread more easily than flu and causes more serious illnesses in some people. It can also take longer before people show symptoms and people can be contagious for longer. More information about differences between flu and COVID-19 is available in the different sections below.

Because some of the symptoms of flu and COVID-19 are similar, it may be hard to tell the difference between them based on symptoms alone, and testing may be needed to help confirm a diagnosis.

While more is learned every day about COVID-19 and the virus that causes it, there is still a lot that is unknown . This page compares COVID-19 and flu, given the best available information to date.



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