|Year : 2021 | Volume
| Issue : 3 | Page : 310-314
Strategies in laboratory diagnosis of COVID-19 in India
Abhijit Vinodrao Boratne1, Lalithambigai Chellamuthu1, Yogesh Bahurupi2
1 Department of Community Medicine, Mahatma Gandhi Medical College and Research Institute, Puducherry, India
2 Department of Community and Family Medicine, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India
|Date of Submission||28-Nov-2020|
|Date of Acceptance||22-May-2021|
|Date of Web Publication||30-Sep-2021|
Dr. Lalithambigai Chellamuthu
Department of Community Medicine, Mahatma Gandhi Medical College and Research Institute, Puducherry - 607 402
Source of Support: None, Conflict of Interest: None
COVID-19 has been documented as the fifth pandemic since 1918 Spanish flu (H1N1). It began as a human cluster of pneumonia cases of unknown etiology, reported from Wuhan, China, during late December 2019. The etiological agent of the pandemic was detected as severe acute respiratory syndrome coronavirus-2. The Indian Council of Medical Research along with the Ministry of Health and Family Welfare expanded and diversified testing capacity. Reverse transcription-polymerase chain reaction (RT-PCR) is the gold standard for COVID-19 diagnosis. TrueNat or cartridge-based nucleic acid amplification test is for testing at primary and secondary health care level. Rapid antigen test has been designated for field level testing in containment zones as well as hospitals supplementary to RT-PCR. Antibody testing had been adopted mainly for surveillance purpose and not for confirmation of COVID-19.
Keywords: Antibody testing, COVID-19, laboratory diagnosis, rapid antigen test, reverse transcription-polymerase chain reaction
|How to cite this article:|
Boratne AV, Chellamuthu L, Bahurupi Y. Strategies in laboratory diagnosis of COVID-19 in India. Indian J Health Sci Biomed Res 2021;14:310-4
| Introduction|| |
COVID-19 has been documented as the fifth pandemic since 1918 Spanish flu (H1N1). It began as a human cluster of pneumonia cases of unknown etiology, reported from Wuhan, China, during late December 2019. The etiological agent of the was detected to be novel coronavirus and the outbreak was declared as a Public Health Emergency of International Concern on January 30, 2020, by the World Health Organization (WHO). The global assessment was carried out by WHO and announced COVID-19 as a pandemic on March 11, 2020. For handling this crisis in the best possible way, there is a need for adopting a strategic plan in each country. Laboratory tests play a vital role in getting patient's accurate diagnosis regardless of the presence of symptoms, provision of effective care, and at no time has their importance been clearer than during the current pandemic. Therefore, this article gives an outline on various strategies adopted by India for testing of COVID-19.
| Importance of Laboratory Diagnosis in the Pandemic Situation|| |
The novel coronavirus responsible for the ongoing pandemic was temporarily named as 2019-nCoV. Later, whole-genome sequencing results showed that novel coronavirus was genetically related to the coronavirus responsible for severe acute respiratory syndrome (SARS) outbreak during 2003. Hence, the virus was renamed as SARS coronavirus-2 (SARS-CoV-2). The epidemiological link of SARS-CoV-2 still seems to be missing, although initial cases had been associated with seafood market. The genome sequencing demonstrated similarity between SARS-CoV-2 and another coronavirus isolated from bat species. Pangolins were also suggested to be the natural host of coronavirus by some studies. Either human-to-human transmission or zoonotic origin was suspected to be the source for coronavirus. Eventually, evidence of human-to-human transmission became strongly supported by January 2020 after a field visit conducted by a WHO team to the Wuhan city of China.
| Route of Transmission and Clinical Implications of COVID-19|| |
Initially, SARS-CoV-2 was considered to be transmitted through human-to-human by respiratory droplets, close contact with diseased patients, and possibly by fecal-oral and aerosol contact. Later, airborne transmission was referred to be the dominant route for the spread of the disease.
In one of the early studies in the city of Wuhan, the mean incubation period for COVID-19 was observed to be 5.2 days, though it might vary widely with individuals with a maximum cut-off up to 14 days. Majority (80%) of SARS-CoV-2 affected persons were said to be asymptomatic or presents with mild symptoms. Evidence revealed that those asymptomatic individuals can transmit the disease to others. On the other hand, many studies reported different clinical manifestations of covid-19. The most common symptoms included fever, cough, dyspnea, malaise, fatigue, and sputum/secretion. Neurological symptoms, dermatological manifestations, anorexia, myalgia, sneezing, sore throat, rhinitis, headache, chest pain, and diarrhea were other common manifestations. Some symptomatic people especially those with co-morbidities clinically deteriorated and eventually faced death.,
| Sample Collection and Testing for COVID-19|| |
Respiratory samples were found to have the greatest yield, while the virus was possibly detected in other specimens as well, such as stool and blood. Recommendations for respiratory samples were either or both of the following specimens:
- Upper respiratory specimens: Nasopharyngeal and oropharyngeal swab/wash in ambulatory patients
- Lower respiratory specimens: Sputum (if productive cough present) and/or endotracheal aspirate or bronchoalveolar lavage in patients with severe respiratory disease.
In addition, blood and stool specimens were advised for collection based on viral shedding patterns of COVID-19 which were similar to SARS and Middle East Respiratory Syndrome. Retrospectively, for the identification of cases among survived persons, paired serum (acute and convalescent) was suggested. In case of deceased patients, autopsy material including lung tissue was considered. Decision to test a patient for COVID-19 was based on clinical and epidemiological factors. PCR testing of asymptomatic or mildly symptomatic contacts was prescribed. Protocols for screening were adopted with regard to local situations. Case definitions were being regularly reviewed and updated by the WHO. Suspect cases were subjected to screening for virus with nucleic acid amplification tests (NAAT), namely, reverse transcription-polymerase chain reaction (RT-PCR). If case management demands, patients were tested for other respiratory pathogens using routine laboratory investigations as recommended in local management guidelines for community-acquired pneumonia ensuring no delay in testing for COVID-19. Clinical specimen handling, collection, storage, and transport adhered to the guidelines issued by WHO.
| Scaling Up of Laboratory Testing for COVID-19 in India|| |
The Indian Council of Medical Research (ICMR) along with the Ministry of Health and Family Welfare expanded and diversified testing capacity. India launched COVID-19 testing facilities to ramp up the diagnostic capacity as well as strengthen screening and treatment. With the vision of “Atmanirbhar Bharat” (self-reliant India) and “Make in India”, indigenous vendors and manufacturers of India were supported to produce swabs for sample collection and molecular diagnostic platforms such as RNA extraction and RT-PCR kits.
| Testing Strategy for COVID-19 in India|| |
In March 2020, India formulated its first testing strategy and revised in couple of days which insisted on five testing criteria for COVID-19. Guidelines and Standard Operating Procedures were published by the National Institute of Virology, Pune, under the ICMR, for private sector laboratories intending to initiate COVID-19 testing. In April 2020, there was an addition to the existing testing strategy for COVID-19 which mentioned testing of all symptomatic ILI (Influenza Like Illness), within 7 days of illness by RT-PCR and after 7 days of illness by antibody test (if negative, confirmed by RT-PCR) among hotspots/containment zones. During May 2020, there were a few modifications and addition to the previous testing strategy for COVID-19 using RT-PCR. In September 2020, a final revised testing strategy was recommended by the National Task Force on COVID-19 [Table 1].,
| Reverse transcription Polymerase Chain Reaction for COVID-19 in India|| |
RT-PCR is considered to be the gold standard test for the diagnosis of COVID-19. The test demands pre-requisites like specific biosafety precautions to be followed. The average turnaround time for RT-PCR is 4–5 h. The advantage of this test is accuracy with large capacity to run 90 samples at a time and disadvantage being specialized laboratory requirements making it difficult to be performed at every district level laboratory which do not have molecular virology facilities.
| TrueNat and Cartridge Based Nucleic Acid Amplification Test for COVID-19 in India|| |
These tests have widespread availability even at grassroot level (primary and secondary health care facilities) as these platforms are already in use for Tuberculosis and other infectious diseases. These platforms have a turnaround time of 30–60 min but only 1–4 samples can be tested in one run. The viral lysis buffer that comes with COVID-19 cartridges inactivates the virus and poses a minimum biosafety hazard. Safety is further augmented by the closed nature of these platforms and minimum sample handling.
| Rapid Antigen Test|| |
As the public health fraternity is focused on the “test, track, treat” strategy for COVID-19, it is crucial to use reliable field-level antigen-based assays for early detection of infection and quick containment. Most of such tests have relatively moderate sensitivity but high specificity. Standard Q COVID-19 antigen kit and has been developed which does not require a specialized machine and can be interpreted with a naked eye. It is now recommended to use the Standard Q COVID-19 antigen test as a point of care diagnostic assay for testing in containment zones as well as hospitals in combination with the gold standard RT-PCR test. A positive test should be considered as a true positive whereas all symptomatic individuals testing negative through the rapid antigen test (RAT) should be confirmed with a real-time PCR test.
| Antibody Testing for COVID-19 in India|| |
IgG antibody testing strategy for COVID-19 was introduced in April 2020. Antibody testing was mandated only for surveillance purpose and not for diagnosis of COVID-19. IgG antibodies for SARS-CoV-2 usually start appearing after 2 weeks of disease onset or once recovered from infection and last for several months. Therefore, IgG antibody testing has no role in detecting acute infection. However, detection of IgG antibodies may be useful in the following situations:
- Serological surveys (to understand the proportion of the population exposed to infection with SARS-CoV-2)
- The survey in high risk or vulnerable populations (to know who has been infected in the past and has now recovered).
Seventeen vulnerable groups/population for serosurveys using IgG ELISA test were also mentioned in the antibody testing strategy.
| Conclusion|| |
Framing and following the testing strategies for COVID-19 is an excellent step from the Government of India. Furthermore, efforts had been made toward strengthening testing capacity and improving diagnostic accuracy and thereby improving treatment services and outcome of COVID-19 affected patients. RT-PCR has been designated as the gold standard for COVID-19 diagnosis. TrueNat or cartridge-based nucleic acid amplification test have been advised for testing at primary and secondary health care level. RAT has been recommended for field-level testing in containment zones as well as hospitals supplementary to RT-PCR. Antibody testing had been adopted mainly for surveillance purpose and not for confirmation of COVID-19.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
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