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What is a virus: How viruses spread, how they differ from bacteria, and common viral infections

Tue, 14 Dec 2021 07:04:19 +0000

Since the beginning of the COVID-19 pandemic, the word ‘virus’ has become a household term, being used in casual conversation on a day-to-day basis in every corner of the world. But what exactly is a virus? How does it differ from other infectious agents? And are all viruses equal?

Table of contents for this article

What is a virus?

Viruses are small groups of genetic code, such as DNA or RNA, enclosed within a shell of protein. A virus cannot survive or multiply on its own, nor can it obtain or store energy. It requires a living organism, or host, which it must inhabit to perform these functions that are basic to life. Hosts can be bacteria, plants, or animals,including human beings.

The incapability of a virus to survive without a host means that they are classed as non-living entities.

Some viruses, like the coronavirus SARS-CoV-2 behind COVID-19, infect the host for a number of days or weeks before being cleared from the system. Other viruses, like varicella-zoster that causes chickenpox, and the human immunodeficiency virus (HIV), can sit dormant in a host without causing an active infection for a number of years.

Read here to find out what happens when you’ve had a Covid test, from collection to results

How does a virus spread?

Most people are now aware that the SARS-CoV-2 virus can be spread through respiratory infection symptoms such as sneezing and coughing, and can also be spread through actions such as speaking or breathing.

There are four primary forms of transmission in which viruses spread:

1. Airborne transmission: Airborne transmission occurs when infected viral droplets in the air are inhaled by another living organism. Airborne transmission is how COVID-19 is commonly spread.

2. Vehicle transmission: Vehicle transmission occurs when food, water, body fluids, or inanimate objects passively carry the virus and transmit it when they come in contact with a potential host organism.

3. Direct transmission: Direct contact transmission occurs when viral particles are spread through physical contact between an infected and uninfected animal, plant, or human being. Examples include ingesting infected foodstuffs or transmission via kissing or sexual activity.

4. Indirect transmission: Indirect contact transmission occurs when the viral particles are spread via contact with contaminated materials such as unsterile medical equipment.

Difference between Viruses and bacteria

On the surface of it, viruses and bacteria may seem very similar. They are spread from human to human in very similar ways and can have similar ravaging effects on human bodies. However, there are in fact far more differences than similarities between them.

Viruses are much smaller than bacteria, and even the largest virus is tinier than the smallest bacterium.

A virus needs a living host to survive, thrive and multiply. This is not the case for bacteria, and they can live independently in almost any environment.

Treatment for bacterial infection is primarily via antibiotics. Antibiotics do not have an effect on viruses, which are generally treated with anti-viral agents where available.

Vaccines are an important preventive agent against viruses.

Common viral infections

Coronavirus
Influenza – causes ‘the ‘flu’
Rhinoviruses – cause the ‘common cold’
Human papillomavirus (HPV) – causes genital warts and cervical cancer
Varicella-zoster – causes chickenpox
Noroviruses – cause vomiting and diarrhoea
Measles
Mumps

What is the endgame of a virus?

From an evolutionary perspective, the ‘perfect’ virus is one that infects as many hosts as possible to replicate, without killing the host in the process, because the host is needed to aid transmission. The SARS-CoV-2 virus does this very well. Most infected people don’t die from the infection, and it has a relatively long incubation period, which is the time from infection to the point where symptoms are first displayed. This, and the highly effective manner in which it is transmitted through the air, make it a very successful virus.

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Pathology testing key to tracing more infectious strains of COVID-19

Thu, 04 Feb 2021 01:40:51 +0000

A number of new concerning variants of the COVID-19 virus have begun to appear across the globe. The B.1.1.7 strain, commonly referred to as the UK strain of the virus, has now been identified in 40 other countries¹ outside the UK, including Australia.

Referred to as the South African strain, the variant 501Y.V2 or B.1.351, has also appeared in hotel quarantine in New South Wales.

Early research suggests the UK and South African strains spread more easily than previous variants. The UK strain may raise the R value of the virus by at least 0.4. The R value determines the average number of people a person with COVID-19 might pass the infection to. In December 2020 it was reported that B.1.1.7 was responsible for 60% of cases of COVID-19 in London².

Dr Rob Baird talks about genome sequencing for COVID-19 to Channel 7

Dr Robert Baird, Pathology Awareness Australia Ambassador, Director of Microbiology and Infectious Diseases Physician at the Royal Darwin Hospital said:

“The evidence is pointing towards these variants being more transmissible and that means that you only need a smaller infectious ‘dose’ of the virus for someone to become infected. It makes all the COVID infection control protocols even more vital. Settings where it is difficult to have regular cleaning, social distancing and good ventilation, for example, in the public toilets at a large event, or public transport, would become much higher risk if a variant like this is in the community.”

The B.1.1.7 and 501Y.V2 strains carry a larger than usual number of mutations³ to the genetic code. According to the Centers for Disease Control and Prevention⁴, the new variants have several mutations that affect the spike protein on the virus surface that attaches to human cells.

Another variant has also been reported in Japan, found in four travellers from Brazil. This variant is said to have 12 mutations and may show similarities to the B.1.1.7 and 501Y.V2 strains; research is being conducted to learn more.

The main type of test used in pathology laboratories to detect SARS-CoV-2 is the reverse-transcriptase polymerase chain reaction⁵ test, commonly known as PCR. This test is usually performed on a nasal and throat swab sample, and detects the virus’s genetic material in the sample.

Currently, the standard PCR tests used in Australian pathology labs can detect new variants of COVID-19, as the test targets several parts of the virus’s genetic make-up. If further mutations were to occur that significantly alter these testing targets, existing PCR tests may need to be adapted to ensure they are able to detect emerging variants effectively.

Furthermore, vaccinations against COVID-19 could be rendered less effective if mutations continue to emerge that alter the parts of the virus targeted by the vaccine. This is especially true for the 501Y.V2 strain of the virus and it is currently under investigation to ensure the vaccination program will be effective against it.

Infection control is the key to preventing the spread of the virus. If the spread is well controlled the virus will have fewer opportunities to mutate helping to ensure existing tests, vaccines and treatments remain effective.

Dr Baird said: “At the moment, we have been advised the currently approved vaccines in Western countries will be active against the new variants. Continued infection control measures to keep case numbers down will slow the rate of virus mutation. The more people there are infected with the virus, the more opportunities, it has to mutate so the key is to prevent more mutations happening, which may lead to current vaccines needing modification. Overall community vaccination rates may need to be higher for more infectious strains to combat new strains of the virus and to achieve herd immunity.”

Microbiologists use genomic sequencing techniques to identify the virus variants by their DNA or RNA. Genomic testing is different from standard PCR testing because it looks at the entire genetic make-up of the virus.

Dr Baird said:

“I explain it like an alphabet of letters in a book. The coronavirus has about 30,000 letters and when you are doing a PCR test, you’re just looking at a few hundred specific letters to give a positive or negative result. With genome sequencing you get the whole book, and you can compare that copy of the book to another copy and look for any typos (strain variants).”

Genomic testing is widely available in Australia and has been used to detect new strains of COVID-19 within patients who have arrived from overseas, and in areas where outbreaks have occurred.

There have been approximately 8,000 viral genomic sequences performed in Australia since the beginning of the pandemic. The sequences are uploaded to a database known as AUSTRAKKA⁶. Health care workers can use this resource to compare the genomic sequences of new cases, to track existing and emerging mutations, and any variants with characteristics that are concerning, such as B.1.1.7 and 501Y.V2.

The new variants have many potentially important mutations and one of these, N501Y, has made a significant change to the most important part of the spike protein, the receptor building domain³.

Humans have ACE receptors where the virus enters the cells using the spike protein, these receptors change shape over time as we grow up. Some scientists believe the mutations in the B.1.1.7 and 501Y.V2 variants could cause COVID-19 to spread more easily in children than before because the mutated spike protein can access juvenile ACE receptors more easily.

References:

IMAGE CREDIT: The Conversation

The post Pathology testing key to tracing more infectious strains of COVID-19 first appeared on Know Pathology Know Healthcare.

EXPLAINER: How do we know what strains of COVID-19 are circulating in Australia?

Thu, 04 Feb 2021 01:27:41 +0000

Table of Content

What is genome sequencing?
Why do we need genome sequencing for COVID-19?
I tested positive for COVID-19. How do I know which variant I have?
What strains of COVID-19 are circulating in Australia?
How do we know that pathology tests can find all the different COVID-19 strains that are circulating?

With some recent tightening of restrictions caused by cases of the highly infectious UK variant, how do we know what strains of COVID-19 are out there and how can we be sure testing is effectively picking up new strains? The answer is genome sequencing.

What is genome sequencing?

Every living thing is made up of genetic material, DNA or RNA, which contains the code for how that thing is made and functions. The genome is the entirety of this code, which is unique to each individual and expressed in the letters CGAT.

If we think of this code like a large book filled with letters; sequencing the genome is decoding the entire book, compared to other types of genetic testing which might examine just a few specific pages or chapters.

The process to sequence a genome is similar whether it is for a human, a plant or a virus. The major difference is that the human genome is much, much bigger and more complex than the genome of a virus, which is why it takes a lot longer to sequence the human genome and analyse the data.

Why do we need genome sequencing for COVID-19?

The virus needs to be sequenced so that a diagnostic test can be made for it, and to track how it is changing over time.

SARS-CoV-2, the virus that causes COVID-19, first appeared in China. When existing pathology tests ruled out known pathogens, such as influenza, scientists needed to sequence the viral genome so they could determine that it was a new type of coronavirus, and then develop tests to detect it in humans.

The gold standard test used in Australian pathology laboratories for COVID-19 diagnosis is a polymerase chain reaction (PCR) test. The test takes a sample from the nose and throat of the patient which will contain the virus (if it is present), and applies a technique that will cause viral RNA in the sample to be amplified (copied many times). This can then be detected by the PCR instrument.

The PCR test looks for specific targets in the genetic code of the virus and these targets can only be identified, and this specific test created, once the viral genome is known.

I tested positive for COVID-19. How do I know which variant I have?

For most patients who test positive – you won’t know what specific variant of COVID-19 you have. This is because, so far, little clinical difference has been reported between variants. That means that what you should do as a patient to look after yourself and others, and how doctors treat you, won’t change depending on which variant you have.

Although a PCR test can spot certain anomalies in a sample that would indicate the likelihood of a specific strain, the only way to accurately determine which variant the patient is infected with is genome sequencing.

For example, the UK variant known as B.1.1.7 has a particular genetic change identified as H69/V70 deletion. This shows up on the PCR test commonly being used in the UK because it affects a particular part of the spike protein’s genetic code that the PCR test is looking at.¹

When pathologists and medical scientists analyse the test result; they can still detect the presence of SARS-CoV-2 because the test is looking at more than one section of code. Upon seeing the deletion, they might also refer those samples for genome sequencing.

What strains of COVID-19 are circulating in Australia?

The World Health Organisation (WHO) reports that a new variant of SARS-CoV-2 emerged in late January or early February 2020, the D614G strain.

In the following months, this replaced the initial SARS-CoV-2 strain identified in China, and by June 2020 it was the dominant form of the virus circulating globally². The first COVID-19 cases in Australia began appearing in late January 2020³ and by May 2020 around half of the virus samples sequenced in Australia carried the D614G mutation.⁴

Because mutations in the virus are so common and usually do not impact public health advice, the WHO collects and disseminates information on any variants that are reported to have a bearing on how the virus spreads, or clinical implications such as the severity of symptoms, mortality rate and response to treatments and vaccines.

WHO has published information on two ‘variants of concern’ the B.1.1.7 variant which is now widespread in the UK, as well as a variant identified in South Africa known as 501Y.V2. This is similar to the UK variant, but genome sequencing has shown it is distinct from that strain.²

So far, cases of the B.1.1.7 variant first identified in South East England have been reported in Australia and are all linked to hotel quarantine. The South African variant has also spread to other countries, and a small number of cases within the same family unit have been identified in hotel quarantine in New South Wales.

Pathology teams are committed to tracking the virus and suitable samples taken from people coming from overseas are used for genome sequencing. So far, about 8,000 viral genomic sequences have been performed in Australia since the beginning of the pandemic.

The sequences are uploaded to a database known as AUSTRAKKA. These data are used to track outbreaks as well as identify what variants travellers may be bringing into the country.

How do we know that pathology tests can find all the different COVID-19 strains that are circulating?

The pieces of genetic information that the diagnostic PCR tests look at have been carefully selected because they are fundamental parts of the virus and common across variants.

Although mutations occur all the time, these are most often minor changes that do not alter how the virus behaves or presents. The multigene PCR tests used in Australia can still detect the virus even with these mutations.

It would be almost impossible for a significant mutation to occur that affects all the parts of the genetic code targeted by the current PCR tests. To avoid being picked up by a 3 or 4 gene PCR test, those mutations would have to occur in all those targets that the PCR looks for, all at the same time. Such a mutation would be so significant it would likely be considered a new virus altogether.

The surveillance through genome sequencing picks up emerging changes in the viral genetic code, so mutations that affect test targets can be addressed accordingly.

References

IMAGE CREDIT: The Conversation

The post EXPLAINER: How do we know what strains of COVID-19 are circulating in Australia? first appeared on Know Pathology Know Healthcare.