Indian scientists from Massachusetts Institute of Technology (MIT) have claimed to have identified genetic changes in the H1N1 strain from sequences of two samples from India (both from last year). The sequencing information was provided by the National Institute of Virology (NIV) to an international open access flu database.
Indian government agencies like NIV, National Centre for Disease Control (NCDC) and Indian Council of Medical Research (ICMR) have maintained that tests conducted in the current outbreak and in previous years have not established any “significant mutations” in the genes of the H1N1 strain that first surfaced in India in 2009.
The authors of the MIT study — both Indian origin scientists — have said these viruses contain amino acid changes which can be linked to “enhanced virulence and are potentially antigenically distinct from the current vaccine containing 2009 (Cal0709) H1N1” strain.
In an email response to The Indian Express, Dr Ram Sasisekharan, professor of biological engineering and corresponding author of the study said, “The sequences we analysed and discussed in commentary came from public open access flu database as cited in the manuscript. There were only two sequences that NIV deposited in this database for 2014.”
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The scientists have identified three mutations in the 2014 Indian strain — K166Q, T200A in both samples and D225N in one sample — in a type of protein in the virus known as hemagglutinin, which are associated with “increased virulence and disease severity” of the strain.
Terming these findings a “potential cause for concern”, the authors have said “these extensive amino acid changes observed in 2014 Indian influenza HA contradict the recent reports by Indian news media on a lack of mutations observed in the H1N1 viruses in India.”
Dr Sasisekharan, in his email to The Indian Express, also said more information from India in the public database would “help with better management” of the disease. Terming the “nature of India’s influenza surveillance” as “ irregular and reactive”, the MIT scientists have said that of the over 15,000 samples available in public databases, 38.4 per cent comes from the US, while India ranks 14th with “less than 1.5 per cent sequences”.
“Despite the vastness of the Indian subcontinent, only two sequences have been deposited during 2014-2015 from India, suggesting poor surveillance and potentially limiting the response to a deadly outbreak,” the authors have said.
Commenting on the efficacy of existing multi-strain flu vaccines in the market, Dr Sasisekharan said changes were seen in the strains at 15 amino acid positions relative to the vaccine. “With limited sequence information it is hard to say. But if we are using the WHO recommended strain, the HA sequences from the 2014 Indian viruses show changes at 15 amino acid positions relative to the vaccine H1N1 HA. These include changes at critical antigenic sites recognised by the vaccine-elicited neutralising antibodies,” said Dr Sasisekharan.
While additional secretary in the ministry Arun Panda said the government has sought a report from NIV and ICMR on the issue, NIV authorities said they had reviewed the strains mentioned but did not identify any mutations. “Our experts have examined the genome of the strain mentioned in the publication; this is also verified from the information documents received regarding the strains of 2014 from India from Centre for Disease Control and Prevention, Atlanta in December 2014. These reports suggest that there is no such mutation indicating that the current stain has become more pathogenic,” said NIV director D T Mourya.
A senior microbiologist from NCDC in Delhi termed the report as “alarmist”.
NCDC sources countered the MIT authors’ claim of lack of public information about flu strains. “We, together with NIV, have provided over 2000 samples to the WHO database, so this is an altogether unwarranted claim,” said a scientist.
Dr Sasisekharan, however, said this did not include “genome information which is different from strain information”. “What the NIV perhaps is saying is that they have deposited information on number of strains, cases etc,” he said.
Meanwhile, Dr Sujata Baveja, head of microbiology department at KEM hospital in Mumbai, said the mutation is minor.