Friday, June 19, 2020

Laboratory detection of COVID-19 using Real Time RT-PCR

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COVID-19 is an infectious disease caused by severe acute respiratory syndrome corona virus two(SARS-COV2). when the person is infected the most common sign include fever, cough, shortness of breath.
According to the World Health Organization (WHO), the WHO China Country Office was informed of cases of pneumonia of unknown etiology in Wuhan City, Hubei Province, on 31 December 2019. A novel coronavirus currently termed 2019-nCoV was officially announced as the causative agent by Chinese authorities on 7 January. 

What is real time RT-PCR
Real time Reverse Transcriptase Polymerase Chain reaction(real time RT–PCR) is a nuclear-derived method for detecting the presence of specific genetic material in any pathogen, including a virus. Originally, the method used radioactive isotope markers to detect targeted genetic materials, but subsequent refining has led to the replacement of isotopic labelling with special markers, most frequently fluorescent dyes. This technique allows scientists to see the results almost immediately while the process is still ongoing, whereas conventional RT–PCR only provides results at the end of the process.
Real time RT–PCR is one of the most widely used laboratory methods for detecting the COVID-19 virus. While many countries have used real time RT–PCR for diagnosing other diseases, such as Ebola virus and Zika virus, many need support in adapting this method for the COVID-19 virus, as well as in increasing their national testing capacities.
How real time RT PCR works in COVID-19 detection
The sample is collected by nasal pharyngeal swab or oral pharyngeal swab, for nasal pharyngeal  the swab is inserted in the nostril and gently moved forward in the nasal pharynx and then rotated for a specified period of time to collect secretion containing the virus. then the swab is placed immediately in the sterile tube containing the viral transport media.
Because corona virus contain extra ordinary single stranded RNA genome, to detect this virus with PCR, RNA molecule must be converted into complementary DNA by reverse transcriptase. the obtained DNA is then amplified by real time RT-PCR, The sample is treated with several chemical solutions that remove substances such as proteins and fats and that extract only the RNA present in the sample. This extracted RNA is a mix of the person’s own genetic material and, if present, the virus’s RNA.
The RNA is reverse transcribed to DNA using a specific enzyme. then additional short fragments of DNA that are complementary to specific parts of the transcribed viral DNA are added. If the virus is present in a sample, these fragments attach themselves to target sections of the viral DNA. Some of the added genetic fragments are used for building DNA strands during amplification, while the others are used for building the DNA and adding marker labels to the strands, which are then used to detect the virus.
The mixture is then placed in an RT–PCR machine. The machine cycles through temperatures that heat and cool the mixture to trigger specific chemical reactions that create new, identical copies of the target sections of viral DNA. The cycle is repeated over and over to continue copying the target sections of viral DNA. Each cycle doubles the previous number: two copies become four, four copies become eight, and so on. A standard real time RT–PCR set-up usually goes through 35 cycles, which means that, by the end of the process, around 35 billion new copies of the sections of viral DNA are created from each strand of the virus present in the sample.
As new copies of the viral DNA sections are built, the marker labels attach to the DNA strands and then release a fluorescent dye, which is measured by the machine’s computer and presented in real time on the screen. The computer tracks the amount of fluorescence in the sample after each cycle. When a certain level of fluorescence is surpassed, this confirms that the virus is present. Scientists also monitor how many cycles it takes to reach this level in order to estimate the severity of the infection: the fewer the cycles, the more severe the viral infection is.

Sunday, June 14, 2020

Califonia:west Nile virus found in milptus mosquitoes

The COVID-19 pandemic is far from getting contained but it appears other health threats are slowly creeping in. Over in Milipitas, some mosquitoes collected tested positive for the West Nile virus. Crews from the Santa Clara County Vector Control now plan to spray mosquito control treatment in select parts of the region as a preventive measure.
Mosquito control spraying treatment is set to begin on Thursday in affected regions. People residing in affected areas are not required to relocate but urged to remain indoors to avoid exposure. The areas that are affected include the Dixon Landing Road to the north, North Milpitas Boulevard and North Abel Street to the east, Highway 237 and Bellew Drive to the west and North McCarthy Boulevard to the West, CBS reported. Locals will be informed if the treatment will be done in their area via door hangers, phone and email alerts through AlertSSC and social media.
The West Nile virus was originally discovered in 2003. More than 7,000 locals in the area have contracted the virus with 309 dying from it. There are no symptoms caused by the virus but may cause fever, headache and body aches. In extreme cases, the virus can leave people with severe neurological damage or death in some cases.
Similar to the coronavirus, the people at risk of contracting the West Nile virus are the ones aged over 50. People who also have some underlying medical condition such as diabetes, high blood pressure, cancer and kidney-related disease are also at risk of contracting the disease.
Based on the latest reports, it appears that the virus is already spreading with Elk Grove and Illinois revealing mosquitoes also testing positive in their areas. Officials from the Sacramento-Yolo Mosquito Vector Control District confirmed that their sample was taken from an area near Bond Road and Highway 99. The rise in cases is attributed to the warm weather, the time where the number of mosquitoes increase, CBS Sacramento reported.
For bug bite first aid, here are 7 must-have products. Pixabay
"It's important for residents to take these findings seriously and do everything they can to protect themselves," Gary Goodman, district manager, said.
In Illinois, the Des Plaines Valley Mosquito Abatement District collected a positive mosquito batch last May 31 from River Forest. The North Shore Mosquito Abatement District also collected a positive mosquito batch on June 5 in Evanston, KWQC reported.
No human cases have been reported so far but everyone is urged to take the necessary protective measures. This includes wearing insect repellent at all times. Locals are also urged to report dead birds and neglected pools.

Saturday, June 13, 2020

Google's medical diagnosis and advices are "almost" always wrong: New study

Many people turn to 'Dr. Google' to self-diagnose their health symptoms and seek medical advice, but online symptom checkers are only accurate about a third of the time, according to new Edith Cowan University (ECU) research published in the Medical Journal of Australia today.
The study analysed 36 international mobile and web-based symptom checkers and found they produced the correct diagnosis as the first result just 36 per cent of the time, and within the top three results 52 per cent of the time.
The research also found that the advice provided on when and where to seek health care was accurate 49 per cent of the time.
It has been estimated that Google's health related searches amount to approximately 70,000 every minute. Close to 40 per cent of Australians look for online health information to self-treat.
Lead author and ECU Masters student Michella Hill said the findings should give people pause for thought.
"While it may be tempting to use these tools to find out what may be causing your symptoms, most of the time they are unreliable at best and can be dangerous at worst," she said.
Online symptom checkers ask users to list their symptoms before presenting possible diagnoses. Triage advice is about whether—or how quickly—the user should see a doctor or go to hospital.
The 'cyberchondria' effect
According to Ms Hill, online symptom checkers may be providing a false sense of security.
"We've all been guilty of being 'cyberchondriacs' and googling at the first sign of a niggle or headache," she said.
"But the reality is these websites and apps should be viewed very cautiously as they do not look at the whole picture—they don't know your medical history or other symptoms.
"For people who lack health knowledge, they may think the advice they're given is accurate or that their condition is not serious when it may be."
When to see a doctor
The research found that triage advice, that is when and where to seek healthcare, provided more accurate results than for diagnoses.
"We found the advice for seeking medical attention for emergency and urgent care cases was appropriate around 60 per cent of the time, but for non-emergencies that dropped to 30 to 40 per cent," Ms Hill said.
"Generally the triage advice erred on the side of caution, which in some ways is good but can lead to people going to an emergency department when they really don't need to."
A balance
According to Ms Hill, online symptom checkers can have a place in the modern health system.
"These sites are not a replacement for going to the doctor, but they can be useful in providing more information once you do have an official diagnosis," she said.
"We're also seeing symptom checkers being used to good effect with the current COVID-19 pandemic. For example, the UK's National Health Service is using these tools to monitor symptoms and potential 'hot spot' locations for this disease on a national basis."
Lack of quality control
Ms Hill points to the lack of government regulation and data assurance as being major issues behind the quality of online symptom checkers.
"There is no real transparency or validation around how these sites are acquiring their data," she said.
"We also found many of the international sites didn't include some illnesses that exist in Australia, such as Ross River fever and Hendra virus, and they don't list services relevant to Australia."
'The quality of diagnosis and triage advice provided by free online symptom checkers and apps in Australia' was published in the Medical Journal of Australia.
More information: Michella G Hill et al, The quality of diagnosis and triage advice provided by free online symptom checkers and apps in Australia, Medical Journal of Australia (2020). DOI: 10.5694/mja2.50600
Journal information: Medical Journal of Australia

Thursday, June 11, 2020

Clues about Covid-19 among the young and healthy


An investigation of a major coronavirus outbreak aboard the USS Theodore Roosevelt aircraft carrier may reveal clues as to how Covid-19 affects younger adults.


This is the first major look at Covid-19 infections among healthy young adults that the CDC has released, More than 1,000 of the ship's nearly 4,900-member crew tested positive for Covid-19 following the outbreak. After spending weeks at a port in Guam, the ship returned to sea last month.
The majority -- nearly 60% -- of sailors in the study who had antibodies had neutralizing ones, "a promising indicator of at least short-term immunity.
Most reported mild or no symptoms, and those who took preventive measures -- such as face masks and social distancing -- were less likely to become infected.
What we saw was that most of the infections were actually mild, in addition to those that were asymptomatic, And this is perhaps different from studies of older Americans, or maybe even those who were hospitalized already, and certainly much different from those with underlying health conditions. With a number of young people reporting mild, atypical, or no symptoms from the virus, "symptom-based surveillance might not detect all infections.

 Most tested positive for antibodies

The report, published Tuesday, included a sample of 382 service members, with a median age of 30. According to the report, three-fourths were male. Nearly 60% of them tested positive for antibodies, and among them, 59% had also developed neutralizing antibodies by the time their blood samples were taken. Neutralizing antibodies bind to the virus, potentially disabling it from attacking human cells. In a handful of participants, these antibodies were detected more than 40 days after their symptoms began. However, because the data come from a single point in time, they note that longer studies will be needed to definitively show whether and how long these antibodies might protect against the virus.

 Lower infection rate in those who took protective measures


Those who took preventive measures were also less likely to become infected. Sailors who wore face coverings were less likely to become infected (55.8% versus 80.8%), as were those who avoided common areas (53.8% versus 67.5%) and practiced physical distancing (54.7% versus 70.0%). Symptoms more closely associated with Covid-19 in this sample were loss of taste or smell, muscle pain, fever and chills. Two were hospitalized among the 238 in the study confirmed to have been infected with the virus. Officials are working to "tailor our public health practices to the unique characteristics of this adversary whose secret weapon, as you know, is the ability to be transmitted by an individual before they know they're infected.

  Credit CNN.


Monday, June 8, 2020

Breakthrough: Microbe found to block malaria transmission

The malaria disease burden remains a major impediment to economic development over many regions of sub-Saharan Africa. Large-scale insecticide treated net (ITN) distribution campaigns over the previous 15 years have reduced malaria cases by an estimated 40%. However, progress has plateaued; between 2014 and 2016 global incidence remained essentially the same. This a strong indication that current control measures are insufficient and additional novel strategies to control Anopheles mosquito populations or their capacity  to transmit Plasmodium parasites are needed if we are to make further inroads in reducing malaria incidence.
The outcome of vector–pathogen interactions can be influenced by symbiotic microbes. Notably, symbionts can prevent disease vectors from transmitting pathogens that are agents of human disease. This can be developed into a novel vector management strategy; symbionts are disseminated into vector populations to limit their capacity to transmit human disease.
In a research done, Scientists found that microsporidia MB, a fungi-like organism which occurs naturally in malaria-carrying mosquitoes, stops malaria transmission, but does not kill the mosquito. Researchers found this symbiotic microsporidia at moderate levels in wild Anopheles arabiensis mosquitoes in Kenya. When these mosquitoes were fed Plasmodium falciparum-infected blood, the microsporidia prevented the formation of oocysts in the mosquito. Sporozoites, the form of the parasite that are injected into humans during a blood meal, develop within oocysts. Disrupting oocyst formation, therefore, disrupts malaria transmission. The problem is that microsporidia MB is found in less than 10% of wild Anopheles arabiensis mosquitoes in Kenya, with greatest prevalence after peak rainfall. The aim now is to design ways to increase the presence and dissemination of this microsporidia so it can disrupt transmission.

Saturday, June 6, 2020

Harmful and wonderful Prtotozoa

Protozoans: Useful and Harmful Protozoans
you may have seen some of these unicellular organisms in the drop of pond water you observed under the microscope. They are traditionally looked upon as animals, because most protozoans are animal-like. 'Protozoa', in fact, means 'the first animal'. Even protozoans like Euglena, which contain chlorophyll and can photosynthesise, lack a cell wall.
The others are either saprophytic or parasitic. Some live in freshwater, some in salt water, and some in the soil. Many live in the bodies of animals and plants. Protozoans are the link in the food chain between unicellular algae and small aquatic organisms. In other words, they eat algae and are eaten by small fish and other organisms. They reproduce by binary fission.

Perhaps you remember that Amoeba engulfs food with the help of pseudopodia. It is the simplest of protozoans, found in the soil and freshwater bodies. Paramoecium is another freshwater protozoan found in ponds and ditches. It has hair-like projections, called cilia, which help it swim. They also help to direct food and water into the oral groove of this organism.
Useful protozoans:
1. Protozoans serve as food for many small aquatic organisms. Zooplankton are tiny protozoans which live in the sea. They form the principal diet of blue whales, who gulp them in with sea water.
2. They are the ultimate decomposers in nature, as they feed on bacteria and fungi, which decompose dead organic matter. They are, thus, useful in the treatment of sewage.
3. Some protozoans live in the body of other organisms and help them. Termites, for example, have protozoans living in their body. The protozoans digest the cellulose in the wood eaten by termites and convert it into carbohydrates that the termites can use.
Harmful protozoans:
Some protozoans cause diseases. The protozoan Entamoeba histolytica causes amoebiasis (amoebic dysentery) in human beings, Giardia causes giardiasis (dysentery), while Plasmodium causes malaria. trypanosome, a parasitic protozoan which lives in the bloodstream of human beings, cattle and other animals, causes a dangerous disease called sleeping sickness.