Is it COVID or the Flu or some other infection?


This monsoon, we observe that patients with Fever, Sore throat, and a persistent cough are increasing. The doctors suspect it to be  COVID-19, but the Covid RT-PCR reports are negative. Finding out whether it is COVID or the Flu is important since it changes the entire line of treatment.

Monsoon indeed brings a blissful climate but it also brings risk to various infections that are easily spread in the community. Patients present with COVID-19 like symptoms but are later diagnosed with either the flu or other bacterial infections. It is important to understand whether it is COVID or the flu.

This may happen due to several respiratory pathogens causing a similar spectrum of diseases and are nearly indistinguishable from COVID-19.

Here are a few case studies which we have seen:

Case Number 1:

A 42-year-old female shows symptoms like fever, cough, weight loss, and dyspnoea(difficulty breathing). Clinically, it seemed to be Viral Pneumonia, possibly COVID-19 related to Organising pneumonia.

The doctor started steroids and antihistamines.

However, the condition did not improve. Hence a BioFire Respiratory Panel was prescribed.

On diagnosis, the Result came positive for Mycoplasma and Adenovirus.

She was then treated as a case of atypical pneumonia and started with Clarithromycin and Steroids.  

Case Number 2:

An 85-year-old lady living with her 57-year-old Cousin:

Former presented with Fever, Cough, Hemoptysis(blood in sputum) & later showed

abdominal pain and body ache

The Doctor Ordered an RT-PCR test for COVID-19. However, the results were negative.

The doctors suspected Tuberculosis and were about to start therapy with AKT.

They ordered a GenXpert test which came negative. Post which for further diagnosis they ordered a BIOFIRE Respiratory panel

This time, the reports tested positive with H1N1 Swine flu Infection detected

We thus recommend a BioFire RESPIRATORY PANEL if a SARS RT-PCR is negative and the patient has moderate to severe symptoms or needs hospitalization.

Method of Diagnosis to differentiate between COVID or the Flu or other bacterial\viral infections:

Method used for diagnosis in BioFire Panel is Multiplex Nucleic Acid Detection Test:

checking traces of 20 organisms that can cause these flu-like symptoms. Here are some pathogens listed below -

  •  Adenovirus
  • Coronavirus HKU1, NL63, 229E, OC4
  • Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2),
  • Human Meta pneumonia virus,
  • Human Rhinovirus/Enterovirus,
  • Influenza A & B,
  • Parainfluenza virus 1,2,3 and 4,
  • Respiratory Syncytial virus,
  • Bordetella pertussis,
  • Bordetella parapertussis,
  • Chlamydophila pneumonia and
  • Mycoplasma pneumonia.

Sample Type

BioFire Respiratory Panel - Nasopharyngeal swab, throat swab, sputum, endotracheal secretion, or BAL in a VTM (Viral Transport Medium)

On the other hand, flu is a highly contagious infection of the nose, throat, and lungs. The clinical symptoms observed in Flu-like cases are  mild to moderate fever, sore throat, body ache, lethargy, muscle pain, runny nose, loss of smell sensation, headache, or cough with expectoration  similar to COVID-19


1.Sputum smear study

2.Culture and sensitivity testing for organisms from throat or lung

3.Multiplex PCR testing with BioFire: sensitive (97.1%), specific (99.3%), results within 1.5 hours.

The rapid respiratory PCR test results may enable better-informed and quick diagnosis and treatment of patients. Quick turnaround on a broad menu of pathogens may also help clinicians make vital decisions regarding admission, isolation, and additional diagnostic testing.

It is clear from the above case scenarios that the Biofire respiratory panel is important in deciding the line of TARGETED THERAPY as it identifies the organism responsible for infection and decrease in days of antibiotic use (2.6 days per patient)[2].

Why is a Flu vaccine important?

 1.Flu is a highly contagious illness. A variety of viruses cause the Flu. Hence, the best prevention is to get oneself vaccinated every year.

2.CDC reports, between 140,000 and 810,000 people are hospitalized annually with flu.

3..Seasonal flu and COVID are similar in their clinical presentations.

4.These Flu viruses usually cause the most severe illness during colder months. Thus taking the dose 3-6 months before the Flu Season is advisable.

5.The flu vaccine will protect oneself and protect the people and community around by forming antibodies.

6.Since elderly people, babies, and people with health conditions like asthma are more at risk-taking flu vaccine will help them fight the infection better.

7.The Flu vaccine also turns to be Possible protection against COVID-19 in children: It is seen that flu vaccination can offer some protection to children against COVID by “viral interference -i.e. growth of one virus can be inhibited by previous viral infection, in this case, an inactivated flu virus vaccine.[4]

Types of Flu Vaccines

In India 2 types of Flu vaccines are available -

Standard dose trivalent inactivated influenza vaccine and Standard dose quadrivalent IIV(LAIV).

The LAIV (Live attenuated influenza vaccine) is recommended by nasal route under special circumstances.

Experts recommended the use of quadrivalent IIV over trivalent IIV in developing nations such as India (Grade 2A)

Dose: They are administered as a single dose of 0.5 mL.

Precautions for a Flu Vaccine

  • Patients with a history of a severe allergic reaction (egg allergies) to any components of the vaccine
  • Previous history of Guillain–Barré syndrome (GBS)
  • Patients on Statins have a propensity to reduce the effectiveness of the vaccine
  • Patients suffering from MS(Multiple Sclerosis) should avoid live flu vaccines; inactivated vaccines can be given
  • LAIV should be administered four weeks after another live vaccine, while injectable ones should be given at the different anatomical site
  • Side Effects of vaccine: Few recipients can experience headache, weakness or injection site reactions like pain, swelling or redness.

Recommendations for Flu Vaccines in India

Age Group (in years)         Influenza vaccination recommendation
18-49                  1 dose of IIV/LAIV annually.
 >50   1 Dose annually. Vaccination is strongly recommended for patients at high risk of Influenza.


Tests to consider when you have Covid or Flu related symptoms

Test NameCovid RT PCRCOVIFLUBioFire Upper Respiratory Panel
ComponentSevere Acute Respiratory Syndrome
Coronavirus 2 (SARS-CoV-2) By Real Time PCR Method
. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by Real Time PCR Method
. Influenza A
. Influenza B
. Influenza A H1N1
. Influenza A H3N2
This test detects 20 pathogens using Real Time PCR method
. AdenovirusCoronavirus HKU1, NL63, 229E, OC4
. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
. Human Meta pneumonia virus
. Human Rhinovirus/Enterovirus
. Influenza A & B
. Parainfluenza virus 1,2,3 and 4
. Respiratory Syncytial virus
. Bordetella pertussis
. Bordetella parapertussis
. Chlamydophila pneumonia
. Mycoplasma pneumonia
PriceRs. 800/-Rs. 6000/-Rs. 16000/-

To read more about COVID-19 vs the Flu please read this article from the CDC.


Biofire reference link:

[2] Woo C, Chiu S, Seto W, Peiris M. Cost-effectiveness of rapid diagnosis of viral respiratory tract infections in pediatric patients. J. Clin. Microbiol. 1997;(35):1579–1581




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