COVID19 Diagnostic tests

By Dr Deepu Changappa Cheriamane


The definitive test for SARS-CoV-2 is the real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test. It is believed to be highly specific, but with sensitivity reported as low as 60-70% and as high as 95-97%. Meta-analysis has reported the pooled sensitivity of RT-PCR to be 89%. Thus, false negatives are a real clinical problem, and several negative tests might be required in a single case to be confident about excluding the disease.
Its sensitivity is predicated on time since exposure to SARS-CoV-2, with a false negative rate of 100% on the first day after exposure, dropping to 67% on the fourth day. On the day of symptom onset (~4 days after exposure) the false negative rate remains at 38%, and it reaches its nadir of 20% three days after symptoms begin (8 days post exposure). From this point on, the false negative rate starts to climb again reaching 66% on day 21 after exposure.

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COVID clinical presentation

By Dr Deepu Changappa Cheriamane

Clinical presentation
COVID-19 typically presents with systemic and/or respiratory manifestations. Some individuals infected with SARS-CoV-2 are asymptomatic and can act as carriers. Some also experience mild gastrointestinal or cardiovascular symptoms, although these are much less common. 
The full spectrum of clinical manifestation of COVID-19 remains to be determined. Symptoms and signs are non-specific:
fever (85-90%)
cough (65-70%)
disturbed taste and smell (40-50%) 
fatigue (35-40%)
sputum production (30-35%)
shortness of breath (15-20%)
Less common
myalgia/arthralgia (10-15%)
headaches (10-36%)
sore throat (10-15%)
chills (10-12%)
pleuritic pain
nausea, vomiting, nasal congestion (<10%), diarrhea (<5%)
palpitations, chest tightness
hemoptysis (<5%)
confusion, seizures, paraesthesia, altered consciousness
stroke(most commonly cryptogenic)
COVID-19 sufferers have reported high rates of disturbances of smell and taste, including anosmia, hyposmia, ageusia, and dysgeusia. The numbers of patients affected vary and current evidence points more towards a neurological than a conductive cause of the olfactory dysfunction. 
Various reports suggest patients with the disease may have symptoms of conjunctivitis, and those affected, may have positive viral PCR in their conjunctival fluid. However a meta-analysis of over 1,100 patients found that conjunctivitis was only present in 1.1% cases. A small case series found conjunctivitis to be the only clinical manifestation in some patients with COVID-19.
Cutaneous lesions may also be seen, similar to many other viral infections. In a cohort of 88 patients, 20% developed skin disease, most commonly an erythematous rash. Most of the skin abnormalities were self-limited, resolving in a few days.
In the main, the clinical presentation in children with COVID-19 is milder than in adults. Symptoms are similar to any acute chest infection, encompassing most commonly pyrexia, dry cough, sore throat, sneezing, myalgia and lethargy. Wheezing has also been noted. Other less common (<10%) symptoms in children included diarrhea, lethargy, rhinorrhea and vomiting.
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COVID - Epidemiology

By Dr Deepu Changappa Cheriamane

As of July 2020, the number of cases of confirmed COVID-19 globally is over 11 million affecting virtually every territory, other than isolated South Pacific island states and Antarctica, according to an online virus tracker created by the medical journal, The Lancet, and hosted by Johns Hopkins University. As of June 2020, the United States had more than two million cases, Brazil more than one million, with Russia and India with >500,000 cases. 

The R0 (basic reproduction number) of SARS-CoV-2 has been estimated between 2.2 and 3.28 in a non-lockdown population, that is each infected individual, on average, causes between 2-3 new infections. 
The incubation period for COVID-19 was initially calculated to be about five days, which was based on 10 patients only. An American group performed an epidemiological analysis of 181 cases, for which days of exposure and symptom onset could be estimated accurately. They calculated a median incubation period of 5.1 days, that 97.5% became symptomatic within 11.5 days (CI 8.2 to 15.6 days) of being infected, and that extending the cohort to the 99th percentile results in almost all cases developing symptoms in 14 days after exposure to SARS-CoV-2.
As of June 2020 the number of deaths from COVID-19 passed half a million globally. The case fatality rate is ~2-3%. It is speculated that the true case fatality rate is lower than this because many mild/asymptomatic cases are not being tested, which thus skews the apparent death rate upwards.
A paper published by the Chinese Center for Disease Control and Prevention (CCDC) analyzed all 44,672 cases diagnosed up to 11 February 2020. Of these, ~1% were asymptomatic, and ~80% were classed as "mild". 
Another study looked at clinical characteristics in COVID-19 positively tested close contacts of COVID-19 patients. Approximately 30% of those COVID-19 positive close contacts never developed any symptoms or changes on chest CT scans. The remainder showed changes in CT, but ~20% reportedly developed symptoms during their hospital course, none of them developed severe disease. This suggests that a high percentage of COVID-19 carriers are asymptomatic.
In the Chinese population, 55-60%% of COVID-19 patients were male; the median age has been reported between 47 and 59 years.
Children seem to be relatively unaffected by this virus, or indeed other closely-related coronaviruses.with large cohort studies reporting that 1-2% of COVID-19 patients are children. However, there have been cases of critically-ill children with infants under 12 months likely to be more seriously affected. A very low number of pediatric deaths has been reported . In children, male gender does not seem to be a risk factor. The incubation period has been reported to be shorter than in adults, at about two days.


By Dr Deepu Changappa Cheriamane

The World Health Organization originally called this illness "novel coronavirus-infected pneumonia (NCIP)", and the virus itself had been provisionally named "2019 novel coronavirus (2019-nCoV)" .
On 11 February 2020, the WHO officially renamed the clinical condition COVID-19 (a shortening of COronaVIrus Disease-19) 15. Coincidentally, on the same day, the Coronavirus Study Group of the International Committee on Taxonomy of Viruses renamed the virus "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2). The names of both the disease and the virus should be fully capitalized, except for the 'o' in the viral name, which is in lowercase. 
The official virus name is similar to SARS-CoV-1, the virus strain that caused epidemic severe acute respiratory syndrome (SARS) in 2002-2004, potentially causing confusion 38. The WHO has stated it will use "COVID-19 virus" or the "virus that causes COVID-19" instead of its official name, SARS-CoV-2 when communicating with the public.



By Dr Deepu Changappa Cheriamane


COVID-19 (coronavirus disease 2019) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a strain of coronavirus. The first cases were seen in Wuhan, China, in December 2019 before spreading globally, with more than 11 million cases now confirmed. The current outbreak was officially recognized as a pandemic by the World Health Organization (WHO) on 11 March 2020.

Bandana Face Covering (no sew method) Materials

By Dr Deepu

Bandana (or square cotton cloth approximately 20”x20”)
Rubber bands (or hair ties)
Scissors (if you are cutting your own cloth)

Quick Cut T-shirt Face Covering (no sew method)

By Dr Deepu


1. How to make see mask
2. How to make bandana Mask

Sewn Cloth Face Covering

By Dr Deepu

Two 10”x6” rectangles of cotton fabric
Two 6” pieces of elastic (or rubber bands, string, cloth strips, or hair ties)
Needle and thread (or bobby pin)
Sewing machine
1. Cut out two 10-by-6-inch rectangles of cotton fabric. Use tightly woven cotton, such as quilting fabric or cotton sheets. T-shirt fabric will work in a pinch. Stack the two rectangles; you will sew the mask as if it was a single piece of fabric.

2. Fold over the long sides ¼ inch and hem. Then fold the double layer of fabric over ½ inch along the short sides and stitch down.

3. Run a 6-inch length of 1/8-inch wide elastic through the wider hem on each side of the mask. These will be the ear loops. Use a large needle or a bobby pin to thread it through. Tie the ends tight.
Don’t have elastic? Use hair ties or elastic head bands. If you only have string, you can make the ties longer and tie the mask behind your head.

4. Gently pull on the elastic so that the knots are tucked inside the hem. Gather the sides of the mask on the elastic and adjust so the mask fits your face. Then securely stitch the elastic in place to keep it from slipping.
Learn how to make non sewn face mask in next post

How to Wear a Cloth Face Covering

By Dr Deepu

Cloth face coverings should—
  • fit snugly but comfortably against the side of the face
  • be secured with ties or ear loops
  • include multiple layers of fabric
  • allow for breathing without restriction
  • be able to be laundered and machine dried without damage or change to shape
CDC recommends wearing cloth face coverings in public settings where other social distancing measures are difficult to maintain (e.g., grocery stores and pharmacies), especially in areas of significant community-based transmission.
CDC also advises the use of simple cloth face coverings to slow the spread of the virus and help people who may have the virus and do not know it from transmitting it to others.  Cloth face coverings fashioned from household items or made at home from common materials at low cost can be used as an additional, voluntary public health measure.

Cloth face coverings should not be placed on young children under age 2, anyone who has trouble breathing, or is unconscious, incapacitated or otherwise unable to remove the mask without assistance.
The cloth face coverings recommended are not surgical masks or N-95 respirators.  Those are critical supplies that must continue to be reserved for healthcare workers and other medical first responders, as recommended by current CDC guidance.

Should cloth face coverings be washed or otherwise cleaned regularly? How regularly?
Yes. They should be routinely washed depending on the frequency of use.

How does one safely sterilize/clean a cloth face covering?
A washing machine should suffice in properly washing a face covering.

How does one safely remove a used cloth face covering?
Individuals should be careful not to touch their eyes, nose, and mouth when removing their face covering and wash hands immediately after removing.

Read the next article on how to prepare face mask at home

Hopes raise as new data released on hydroxychloroquine treatment for COVID-19.

By Dr Deepu

The new study, of which the abstract was released today, was performed at IHU Méditerranée Infection, Marseille, France. A cohort of 1061 COVID-19 patients, treated for at least 3 days with the Hydroxychloroquine-Azithromycin (HCQ-AZ) combination and a follow-up of at least 9 days was investigated.
Key findings are:
No cardiac toxicity was observed.
A good clinical outcome and virological cure was obtained in 973 patients within 10 days (91.7%).
A poor outcome was observed for 46 patients (4.3%); 10 were transferred to intensive care units, 5 patients died (0.47%) (74-95 years old) and 31 required 10 days of hospitalization or more.
The authors conclude that:
“The HCQ-AZ combination, when started immediately after diagnosis, is a safe and efficient treatment for COVID-19, with a mortality rate of 0.5%, in elderly patients. It avoids worsening and clears virus persistence and contagiosity in most cases.”

In a recent survey, most physicians worldwide considered that hydroxychloroquine (HCQ) and azithromycin (AZ) are the two most effective drugs among available molecules against COVID-19. Nevertheless, to date, one preliminary clinical trial only has demonstrated its efficacy on the viral load. Additionally, a clinical study including 80 patients was published, and in vitro efficiency of this association was demonstrated.
The study was performed at IHU Méditerranée Infection, Marseille, France. A cohort of 1061 COVID-19 patients, treated for at least 3 days with the HCQ-AZ combination and a follow-up of at least 9 days was investigated. Endpoints were death, worsening and viral shedding persistence.
From March 3rd to April 9th, 2020, 59,655 specimens from 38,617 patients were tested for COVID-19 by PCR. Of the 3,165 positive patients placed in the care of our institute, 1061 previously unpublished patients met our inclusion criteria. Their mean age was 43.6 years old and 492 were male (46.4%). No cardiac toxicity was observed. A good clinical outcome and virological cure was obtained in 973 patients within 10 days (91.7%). Prolonged viral carriage at completion of treatment was observed in 47 patients (4.4%) and was associated to a higher viral load at diagnosis (p <1/100) but viral culture was negative at day 10 and all but one were PCR-cleared at day 5. A poor outcome was observed for 46 patients (4.3%); 10 were transferred to intensive care units, 5 patients died (0.47%) (74-95 years old) and 31 required 10 days of hospitalization or more. Among this group, 25 patients are now cured and 16 are still hospitalized (98% of patients cured so far). Poor clinical outcome was significantly associated to older age (OR 1.11), initial higher severity (OR 10.05) and low hydroxychloroquine serum concentration. In addition, both poor clinical and virological outcomes were associated to the use of selective beta-blocking agents and angiotensin II receptor blockers (P<0.05). Mortality was significantly lower in patients who had received > 3 days of HCQ-AZ than in patients treated with other regimens both at IHU and in all Marseille public hospitals (p< 1/100).
The HCQ-AZ combination, when started immediately after diagnosis, is a safe and efficient treatment for COVID-19, with a mortality rate of 0.5%, in elderly patients. It avoids worsening and clears virus persistence and contagiosity in most cases.

When and how to wear medical masks to protect against coronavirus

By Dr Deepu

Before putting on a mask, clean hands with alcohol-based hand rub or soap and water.
Cover mouth and nose with mask and make sure there are no gaps between your face and the mask.
Avoid touching the mask while using it; if you do, clean your hands with alcohol-based hand rub or soap and water.
Replace the mask with a new one as soon as it is damp and do not re-use single-use masks.
To remove the mask: remove it from behind (do not touch the front of mask); discard immediately in a closed bin; clean hands with alcohol-based hand rub or soap and water.

COVID -19 update

By Dr Deepu


Coronaviruses (CoV) are a large family of viruses that cause illness ranging from the common cold to more serious diseases such as Severe Acute Respiratory Syndrome (SARS-CoV).
The 2019 novel coronavirus is a new strain that has not been seen in humans until now and has caused viral pneumonia. It was first linked to Wuhan’s South China Seafood City market which is a wholesale market for seafood and live animals in December 2019.
The virus has now been detected in several areas throughout China, along with countries across Asia, North and South America, Europe, Africa and Oceana.


You may have noticed different names circulating which relate to the novel corona virus. Below we have listed some of the more common names and explained what they mean.
COVID-19- this is the name for the disease caused by the coronavirus. This is simply short for coronavirus disease 2019. The World Health Organization announced this name on the 11 February 2020.
SARS-CoV-2- severe acute respiratory syndrome-related coronavirus 2. This is the name of the virus, not the disease that results from it. The world Health Organization emphasizes that while the viruses are related, COVID-19 is different from the SARS outbreak of 2003.
Novel corona virus 2019 (nCoV-19)- this was initially used at the start of the outbreak. It refers to the virus which is a novel form of the coronavirus that was first seen in 2019.
Coronavirus- you may see or hear about the virus referred to just as the coronavirus. This is not inaccurate as it is a novel strain of a coronavirus.


The World Health Organization (WHO) advises that the most common symptoms of COVID-19 are fever, tiredness, and dry cough. Some people may experience aches and pains, nasal congestion, runny nose, sore throat or diarrhea. These symptoms are usually mild and begin gradually.
People with pre-existing medical conditions (such as asthma and COPD) are more likely to become severely ill with the virus.


  • Do not touch your mouth, nose or eyes with unwashed hands
  • Try to avoid contact with people who are sick
  • Cover your coughs and sneezes with a tissue and throw it in a bin and
  • Wash your hands thoroughly after touching surfaces that may be contaminated


  • Wet your hands under running water
  • apply soap
  • rub hands together vigorously for at least 20 seconds.
  • make sure you apply soap to all parts of your hands including the backs, between your fingers, fingertips, around and under your nails, thumbs and wrists
  • thoroughly rinse your hands under running water
  • turn off the tap with a paper towel to avoid recontaminating your hands and
  • dry your hands with a disposable paper towel or hand dryer (do not touch the hand dryer).


  • Apply one to two squirts of hand sanitizer to your hands
  • rub all over your hands including: the backs, between your fingers, fingertips, around and under your nails, thumbs and wrists and
  • allow the hand sanitizer to dry. This takes about 20-30 seconds.


Due to the changing nature of travel restrictions, please refer to the World Health Organization for updates.
As symptoms include fever and difficulty breathing, you are advised to speak with a doctor and to make them aware of your travel history if you experience these during or after travel.
Exit screening at international airports and ports in the affected areas may take place to prevent the disease from spreading.

Severe COVID-19 risk could be increased in people with COPD and smokers

By Dr Deepu

People with chronic obstructive pulmonary disease (COPD) and people who currently smoke may have higher levels of a molecule, called angiotensin converting enzyme II (ACE-2), in their lungs according to a study published in the European Respiratory Journal (ERJ).

Previous research shows that ACE-2, which sits on the surface of lung cells, is the ‘entry point’ that allows coronavirus to get into the cells of the lungs and cause an infection.

The new study also shows that levels of ACE-2 in former smokers is lower than in current smokers.

The research was led by Dr Janice Leung at the University of British Columbia and St. Paul’s Hospital, Vancouver, Canada. She said: “The data emerging from China suggested that patients with COPD were at higher risk of having worse outcomes from COVID-19. We hypothesised that this could be because the levels of ACE-2 in their airways might be increased compared to people without COPD, which could possibly make it easier for the virus to infect the airway.”

The team studied samples taken from the lungs of 21 COPD patients and 21 people who did not have COPD. They tested the samples to gauge the level of ACE-2 and compared this with other factors, such whether they were from people who never smoked, were current smokers or former smokers. Not only did they find higher levels of ACE-2 in COPD patients, they also found higher levels in people who were smokers.

The researchers then checked their new findings against two existing study groups, which together contain data on a further 249 people – some non-smokers, some current smokers and some former smokers. Again, they found levels of ACE-2 were higher in current smokers but lower in non-smokers and in those who were former smokers.

Dr Leung said: “We found that patients with COPD and people who are still smoking have higher levels of ACE-2 in their airways, which might put them at an increased risk of developing severe COVID-19 infections. Patients with COPD should be counselled to strictly abide by social distancing and proper hand hygiene to prevent infection.

“We also found that former smokers had similar levels of ACE-2 to people who had never smoked. This suggests that there has never been a better time to quit smoking to protect yourself from COVID-19.”