SCI-ART LAB

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Q: Is TB (tuberculosis) a disease or an infection?  

Krishna: Infection, often the first step, occurs when bacteria, viruses or other microbes that cause disease enter your body and begin to multiply. Disease occurs when the cells in your body are damaged — as a result of the infection — and signs and symptoms of an illness appear.  Tuberculosis (TB) is a potentially serious infectious disease that mainly affects your lungs. The bacteria that cause tuberculosis are spread from one person to another through tiny droplets released into the air via coughs and sneezes but can affect other body parts too.

Q: How do mRNA vaccines work?

Krishna: Vaccines train the immune system to recognize the disease-causing part of a virus. Vaccines traditionally contain either weakened viruses or purified signature proteins of the virus.

mRNA vaccines are new. 

An mRNA vaccine is different, because rather than having the viral protein injected, a person receives genetic material – mRNA – that encodes the viral protein. When these genetic instructions are injected into the upper arm, the muscle cells translate them to make the viral protein directly in the body.

This approach mimics what the SARS-CoV-2 does in nature – but the vaccine mRNA codes only for the critical fragment of the viral protein. This gives the immune system a preview of what the real virus looks like without causing disease. This preview gives the immune system time to design powerful antibodies that can neutralize the real virus if the individual is ever infected.

While this synthetic mRNA is genetic material, it cannot be transmitted to the next generation. After an mRNA injection, this molecule guides the protein production inside the muscle cells, which reaches peak levels for 24 to 48 hours and can last for a few more days.

Q; How does the Lucia test (world's first at home covid 19 testing) work? How reliable it is compared to RT-PCR testing?

Krishna: Are you asking about Lucira COVID-19 All-In-One Test Kit?

This is how it works and it is too technical to understand for the common man (1):

The Lucira COVID-19 All-In-One Test Kit utilizes RT-LAMP technology to detect RNA of the N gene for SARS-CoV-2. This technology can create a signal from a few copies of RNA in less than 30 minutes. The RT-LAMP amplification reaction occurs in two phases, a non-cyclic phase followed by a cyclic phase. During the non-cyclic phase, reverse transcriptase, with RNase H activity, converts the RNA target into cDNA. A DNA polymerase with strand displacement activity then amplifies the cDNA. A successful amplification reaction creates a pH change and subsequently a colour change of the halochromic agents within the reaction mixture. The Sample Vial contains an elution buffer that allows the swab contents to be eluted and lysed at room temperature, releasing viral and human RNA for downstream detection. Upon engagement of the Sample Vial and Test Unit, this eluant enters a fluidic module, contained within the Test Unit that has several individual reaction chambers. The eluant resolubilizes lyophilized reagents, contained within these chambers, which are needed to perform the RT-LAMP reaction. An internal electronic heating element detects this chamber filling and automatically turns on, initiating amplification within the reaction chambers. The reactions are confined within the fluidic unit and no other part of the Test Unit has contact with the sample during amplification. The Test Unit contains chambers that target SARS-CoV-2 RNA (two non-overlapping regions of the N gene), a positive internal control (PIC), and a lysis internal control (LIC). The color change of the reaction mixture is detected in real time using optical and electronic elements contained within the Test Unit. An on-board microprocessor analyzes the color change data to detect the presence of amplification, and hence the target RNA, in each chamber. A diagnostic algorithm, included in the device firmware, is then used to determine patient infectivity status and the results are shown via LED indicators. Results for the test are displayed as either positive, negative, or invalid. A positive result may show in as few as 11 minutes; a negative or invalid result will display in 30 minutes. The result display persists for a minimum of 1 hour after the test has finished running.

In laymen terms, the Lucira Covid-19 All-In-One Test Kit involves three steps: swab, stir and detect. Patients put a sample vial in a battery-powered test unit, swab their nostrils, stir the swab in the vial, then press the vial into the test unit. A red or green light will indicate a negative or positive test within 30 minutes.

In clinical trials, 100% of patients were able to perform the test successfully in about two minutes, according to Lucira. The test is molecular, meaning it extracts genetic material from the virus and amplifies it. The other class of tests are antigen tests, which detect viral proteins. They are usually quicker but less accurate. Molecular tests like Lucira’s are 50 to 60 times more sensitive than antigen tests and considered the ‘gold standard’ for determining if someone is infected (2).

False positives are uncommon, according to data presented by Lucira. For positive results, the Lucira test agreed 94.1% of the time with one of the most sensitive FDA-approved tests, the company said. The two tests agreed 100% of the time when excluding samples with low levels of virus. For negative results, the two tests agreed 98% of the time.

This test has been launched for public in US just now and it is FDA approved. We still have to wait to get results about reliability and comparison.

Footnotes:

  1. https://www.fda.gov/media/143808/download#:~:text=of%20the%20Proced....
  2. Lucira Covid-19 test is first to get FDA nod for home use

Q: Can viruses fight against each other?

Krishna: Y-E-S!

Mimivirus-dependent virus Sputnik  is a subviral agent that reproduces in amoeba  cells that are already infected by a certain helper virus; Sputnik uses the helper virus's machinery for reproduction and inhibits replication of the helper virus. It is known as a virophage, in analogy to the term bacteriophage (viruses that attack bacteria and kill them).

Sputnik was first isolated in 2008 from a sample obtained from humans; it was harvested from the contact lens fluid of an individual with keratitis Naturally however, the Sputnik virophage has been found to multiply inside species of the opportunistically pathogenic protozoan Acanthamoeba, but only if that amoeba is infected with the large mamavirus. Sputnik harnesses the mamavirus proteins to rapidly produce new copies of itself.

Sputnik was found to contain genes that were shared by APMV. These genes could have been acquired by Sputnik after the association of APMV with the host and then interaction between the virophage and the viral host. Recombination within the viral factory might have resulted in the exchange of genes. Sputnik is one of the most convincing pieces of evidence for gene mixing and matching between viruses.

The presence of these genes homologous to the mimivirus in Sputnik suggests that gene transfer between Sputnik and the mimivirus can occur during the infection of Acanthamoeba. Therefore, it is hypothesized that the virophage could be a source of vehicle mediating lateral gene transfer between giant viruses, which constitute a significant part of the DNA virus population in marine environments. Moreover, the presence of three APMV genes in Sputnik implies that gene transfer between a virophage and a giant virus is crucial to viral evolution.

In 2016, for classification of Sputnik-like viruses, including Zamilon, genus Sputnikvirus in the family Lavidaviridae has been established by the International Committee on Taxonomy of Viruses.

Other virophages: 

In March 2011, two additional virophages were described: the Mavirus virophage which preys on the giant Cafeteria roenbergensis virus,and the Organic Lake virophage (OLV), found in the salty Organic Lake in Antarctica, and which preys on phycodnaviruses that attack algae.] Zamilon virophage was the first one found infecting a member of Mimiviridae group C (i. e. Mont1 virus), being able to grow also in Mimiviridae group B, but not group A.

All host viruses of the known virophages belong to the group of nucleocytoplasmic large DNA viruses. Studies have been done to show similarities among the various virophages. Homologous genes among virophages include putative FtsK-HerA family DNA packaging ATPase (ATPase), putative DNA helicase/primase (HEL/PRIM), putative cysteine protease (PRSC), putative MCP, and putative minor capsid protein (mCP). These genes are also referred to as conserved core genes although there is sometimes no or very little sequence similarity among these virophages.

Source of virophages: https://en.m.wikipedia.org/wiki/Sputnik_virophage

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