India failed to map the spread of the Delta variant of coronavirus through genome sequencing in early 2021, contributing to an explosion of cases in the summer that resulted in a deadly second wave of the pandemic.
Now, almost a year later, a new variant of the coronavirus, Omicron, has entered the country. First detected in South Africa and Botswana, it is believed to be even more transmissible than Delta.
Fortunately, there is a simpler way to track Omicron’s spread: the S-gene target failure test.
The S-gene target failure test is basically a version of the RT-PCR, the gold standard laboratory test used for Covid-19 detection, which amplifies the RNA in a virus to detect its genetic material. When the test detects the presence of other genes of the Sars-CoV-2 virus, but not the S-gene, it is considered indicative of Omicron infection. (More on the science later.)
Since many countries lack genome sequencing infrastructure to test all Covid-19 samples, on November 27, the World Health Organisation recommended the use of the S-gene target failure test as a proxy method to detect suspected Omicron cases, which can be confirmed through genome sequencing.
In India, the Central government passed on the WHO’s recommendation to state governments through a letter sent on December 3.
While some states like Tamil Nadu, Maharashatra and Gujarat have begun purchasing S-gene target failure test kits, others like Uttar Pradesh are yet to do so.
One bottleneck that governments could face in the future: only one company worldwide has been recommended by the WHO as a supplier of the S-gene target failure kit.
Currently, Omicron has been found in 57 countries. So far, India has detected 32 cases. If the spread intensifies and global demand for the S-gene kits rises, how well placed is India to access them?
How does the S-gene target failure test work?
All RT-PCR test kits confirm the presence of Covid-19 infection but most cannot detect which variant the person is infected with. However, mutations in spike proteins unique to the Omicron make it possible to detect it through the S-gene target failure RT-PCR test.
An RT-PCR testing kit amplifies the RNA in a virus to detect its genetic material. The Sars-CoV-2 virus has several genes: the ORF1a, ORF1b, M-gene, N-gene, S-gene and others. Testing kits usually target two or more of these genes to identify them and confirm if a sample is Covid-19 positive.
The Omicron variant has over 30 mutations in the spike proteins that bind the virus to the host cell, which includes the deletion of two amino acids H69 and V70. Because of this, the S-gene in the virus cannot be detected through RT-PCR testing.
The Taqpath RT-PCR kit, made by Thermo Fisher Scientific, a pharmaceutical company headquartered in the United States, looks for the ORF1a/b, N- and S-gene in a sample. It is the only RT-PCR kit targeting the S-gene that has been approved by the WHO.
When the Taqpath kit is able to detect ORF1 a/b and N-gene but fails to detect S-gene, that is an indication that the virus may be an Omicron variant. This has to be further confirmed through genome sequencing.
The only other variant with a similar mutation which leads to the S-gene not being detected, is Alpha, also called B.1.1.7. Its circulation is low in India.
Apart from the WHO, the Centers for Disease Control and Prevention in the US, the National Institute for Communicable Diseases in South Africa, and other health organisations have noted that using S-gene target failure test can enable faster identification of Omicron cases, particularly in places where genome sequencing capacity is low.
In India, scientists and laboratory staff agree with this assessment. “The S-gene target failure testing kits make it easier to screen suspected Omicron cases, isolate them and prioritise them for genome sequencing,” said Dr Prashant Thakare, the head of the government molecular diagnostic laboratory in Amravati, Maharashtra.
Procuring kits
Thermo Fisher Scientific, manufacturer of the S-gene target failure RT-PCR kit, can manufacture 25 million Taqpath RT-PCR assays, or test kits, per week globally, a spokesperson from the pharmaceutical company said.
“The investments we’ve made since the start of the pandemic enables us to scale our capacity to meet assay demand and enable healthcare bodies to effectively manage the spread of the variant in the country,” Amit Chopra, managing director of the company in India and South Asia, told Scroll.in.
In India, 1,982 labs are authorised to conduct RT-PCR tests. Thermo Fisher executives claimed over 800 labs are using their kits for Covid-19 testing.
While state officials in Maharashtra, Tamil Nadu, Madhya Pradesh and Gujarat confirmed that their labs had placed orders for the S-gene target failure kits from Thermo Fisher, in Uttar Pradesh, the state government is yet to issue a circular to labs to purchase these kits. “We have not purchased the S-gene target failure kits for this purpose yet,” said Dr Gopal Nath, head of the microbiology laboratory in the Banaras Hindu University.
Several private laboratories, too, have started purchasing the S-gene target failure kits from Thermo Fisher, but the exact quantities are not known.
Sachin Salve, vice president in Thyrocare, said their laboratory has switched to using the S-gene target failure test for testing samples of all international passengers. “We ask for the purpose of the test. If it is a sample of an international passenger or close contact, we process it through the Taqpath kit,” he said.
Salve added that so far the supply of kits remains smooth. “But these are early days. Let’s see how Omicron spreads globally and how demand for this kit rises,” he said.
Other private labs remain cautious about placing bulk orders with Thermo Fisher – at roughly Rs 200 per kit, the price of the S-gene target failure RT-PCR kit is much higher than other RT-PCR kits. Since the prices of RT-PCR tests are currently capped by state governments between Rs 400 and Rs 900, labs prefer buying cheaper kits to keep their costs low.
“We are placing an order for more kits, but not a large order since we don’t know the future demand,” said Dr Anupa Dixit, chief scientist at Suburban Diagnostics, a private company based in Mumbai with labs in Maharashtra, Goa and Madhya Pradesh. “We are hoping Thermo Fisher will reduce the rates.”
Sushant Kinra, CEO of Suburban Diagnostics, however, said the company’s labs are using the S-gene target failure test for all samples. “This will help screen suspected cases faster,” he said.
Dr Anurag Agrawal, director of CSIR-Institute of Genomics and Integrative Biology, said the rising demand for S-gene target failure tests will spark interest among other manufacturers, hopefully creating more production capacity for it. Till then, he said laboratories must judiciously use the S-gene target failure kits for international air travellers and contacts of suspected Omicron cases, and not for every local sample, he said.
India is currently testing 10-12 lakh samples a day, down from 60-80 lakh a day conducted in October and November.
Emergence of Omicron sub-lineages
While the S-gene dropout tests serve as a marker for Omicron, there are limitations to it – new evidence suggests it might not be able to detect Omicron sub-lineage BA.2.
Omicron, also called B.1.1.529, has evolved into at least two lineages, BA.1, which closely resembles the parent variant, and BA.2, which has further mutations. S-gene target failure tests can confirm Covid-19 infection in a person with BA.2 variant, but the mutations in BA.2 makes it impossible to detect an S-gene drop out, according to a report in The Guardian.
Agrawal, head of CSIR-Institute of Genomics and Integrative Biology, said that since the S-gene dropout test does not work on identifying BA.2, “genome sequencing is the only confirmatory way to detect Omicron”.
Dr Rajesh Pandey, a scientist at the same institution, said since Omicron is a new variant, intensive sequencing is required in the initial weeks to track its spread. “Scientifically speaking, we sequence to assess how a variant is spreading in a region. Once it becomes widespread or a dominant variant, then sequencing will not provide any new information,” he said. “It is now that we need to sequence well.”
But sequencing numbers in India continue to be low. In January 2020, the health ministry established a network of 10 laboratories called the Indian SARS-CoV-2 Genomic Consortia, or INSACOG, which sequenced 45,000 samples in the first six months.
Almost a year later, the network has grown to 28 laboratories, with 29,495 samples sequenced in two months between October 4 till December 4.
Overall, the scale of genome sequencing remains inadequate for a country the size of India: just 1.26 lakh samples have been sequenced so far.
However, the scale is likely to pick up – on December 1, the Centre has asked all states to send all Covid-19 positive samples to INSACOG laboratories for Omicron screening. This week, India has reported an average of 8,000-10,000 Covid-19 cases everyday.
But genome sequencing is a time-consuming process. Even if all Covid-19 samples are eventually sequenced in India, the S-gene target failure test still remains the fastest way to screen for Omicron cases, experts said.
This reporting was supported by a grant from the Thakur Family Foundation. Thakur Family Foundation has not exercised any editorial control over the contents of this article.