A medical team collects swabs from police personnel and their family members for COVID-19 tests in Borivali, Mumbai, April 7, 2020. Photo: PTI.

One patient fainted after seeing the nasopharyngeal swab before sample collection. Another was turned back because of staff shortage. Backlog,procuring quality collection kits, and prohibitive costs are some common problems associated with collection of nasopharyngeal (NP) and oropharyngeal (OP) samples to test for the novel coronavirus.

Currently, India has almost 4 lakh COVID-19 cases, and increasing by 10,000 per day or so these days even with limited testing (since you cant discover without tests). As of today, there are 960 testing labs around India. If the government intends to keep pace with the speed with which the virus is spreading, it should consider efficient diagnostic options in addition to increasing lab capacity and other control measures.

If its feasible, state health officials should test asymptomatic and mildcases as well to help plan effective isolation measures, including reverse quarantine. A diagnostic method should be scalable locally, nationally and globally. Monitoring progress diagnostically will also aid disease research.

However, the currently used NP and OP methods dont cater to these needs.

Swabbing the nasopharynx is an invasive and almost blind procedure.An NP swab is passed along the floor of the nasal cavity up to the back wall, swirled for a few seconds then drawn out. This procedure is not always pleasant, for the patient or the health worker. If not done correctly, it can injure the person and cause bleeding. It can also elicit sneezing or coughing, generating aerosols with infectious virus particles from a positive patient, exposing the worker to a potential infection.

Likewise, the OP sample, which is collected from the back of the throat, can also induce gagging and coughing. A deviated nasal septum, tumours or nasal polyps can hamper collection.

Then there are the inconsistencies in sample collection. Some centres perform only NP, some only OP (though its less sensitive compared to NP) and some both. Changes in the time of collection also affect test performance. The procedure requires a skilled and dedicated health worker, and a guarantee that their availability wont be affected by staff shortages typical during pandemics. Otherwise, collection centres may simply cut corners or defer testing.

Many healthcare personnel change their entire PPE gear, priced at nearly Rs 1,000 apiece, between swab collections. Irrational use of PPE adds to the tons of biomedical waste being generated. On the other hand, some centres dont have sufficient funds to afford good quality and adequate PPE for frontline staff.

If swabs are not of the right type, they can increase discomfort to patients and also affect test results. For example, a cotton or calcium alginate tip interferes with the polymerase chain reaction (PCR), and a flexible shaft is required to get to the nasopharynx. Although sterile saline is cheaper and accepted by WHO, viral transport medium (VTM) continues to be used widely to transport swabs. (VTM is a specific substance prepared to contain and transport samples containing viruses without damaging the viruses.) Saline and VTM have comparable efficacy in preserving viral RNA, in both refrigerated and frozen specimens, over seven days.

In India, NP and OP swabs are not sold separately without VTM. Moreover, VTM must have adequate and defined quantities of anti-fungal and antibacterial agents to prevent growth of fungi and bacteria that can interfere with a specimens integrity.

There is a global shortage of the right type of good-quality swabs and of VTM. Earlier, swabs used to be imported from the US and China. Last month, India launched Made in India brands by manufacturers in Delhi company and Mumbai. Their swabs reportedly cost less than Rs 5 apiece compared to Rs 20-30 for imported brands. In the private sector, the price of the collection kit with VTM continues to be Rs 180-200, and Rs 4,500-6,000 for one RT-PCR test (all inclusive).

Against this background, we recommend saliva or saline deep-throat lavage or gargled specimens. They have several advantages over swabbing and swab-testing.

The novel coronavirus uses ACE2 receptors, found on some cells in the body, to gain entry into the cells and hijack their resources to replicate. These receptors are found in the respiratory and cardiovascular systems, kidneys, the gastrointestinal tract, testes and in salivary glands.

When we sleep, the secretions in the upper respiratory tract flow backwards while specimens in the lower respiratory tract are drawn upwards. These two substances meet in the deep part of the throat. When you gargle, the gargling liquid can pick up viruses from this part of the throat.

A study from Guangzhou, China, published in April 2020 in the journal Clinical Infectious Diseases found that self-collected throat wash specimens could be more sensitive than NP specimens.

Viral loads from saliva specimens have also been shown to be consistent with clinical progression. A study by researchers at the Yale School of Medicine, of COVID-19 patients and health workers in COVID-19 wards, showed higher sensitivity and less result variation of saliva samples compared to NP swabs.

Obtaining saliva or gargled samples is quick, easy and safe. Some 1-2 ml of deep-throat saliva or a gargled sample with 10 ml of sterile isotonic saline needs to be spit into a sterile collection container. The collection container can be a sterile urine or sputum cup, which are already widely available, in common use and cost Rs 12-15 apiece, much lower than that of a swab kit.

Since it can be self-collected, saliva or gargled samples circumvent the need for skilled health workers at collection centres, minimising their exposure risk, and reduce PPE use.

Some patients need to undergo repeated tests, such as those whose immune systems are suppressed and those with false negative or indeterminate results. Saliva or lavage is a viable alternative in such cases, since repeated swabbing adds to the cost, workload and demand for PPE.

Tuberculosis centres already have good outreach and efficient specimen transport systems to and from Indias hinterlands. COVID-19 sample collection and transport can be modelled on the same lines.

Deep-throat saliva collection is the major sampling method used in outpatient settings and home collections in Hong Kong. Japan has also adopted saliva samples as alternatives to NP swabs. The US Food and Drug Authority has also issued an emergency use authorisation for a saliva-based test for COVID-19 developed at the Human Genetics Institute, Rutgers University, New Jersey.

Like India, many countries of the Global South are in the upward phase of this pandemic, and in desperate need of a cost-effective way to test more of their citizens. But not all of them have the capacity to manufacture swabs and/or other kit components, forcing them to depend on expensive imported kits. They also suffer from PPE and staff shortages. Overall cost reduction is one of the many advantages of saliva or wash testing. Swabs can be reserved for out-patients or for those who cant self collect or produce saliva.

Researchers should consider performing validation studies of self-collected deep throat gargle and saliva samples. These are sensitive, easy and cost-effective methods whose use can be scaled up manyfold in no time.

Dr Vasundhara Rangaswamy is a clinical microbiologist with international experience and a public health activist in Baroda.

Dr K.R. Antony is a consultant of public health, child survival and development in Kochi. He has served with UNICEF and as the director of Chhattisgarhs State Health Resource Centre, and is now an independent monitor for the National Health Mission.

The views expressed here are the authors own.

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