India has recorded nearly 9,000 infections and 882 deaths caused by the H1N1 influenza virus since the January, leaving doctors, scientists and government authorities baffled at their inability to control the “swine flu” it causes. Maharashtra has notched up the highest number of cases and deaths. Tamil Nadu, Karnataka, Telangana and Kerala have also badly hit.

It’s clear that India has been floundering in its efforts to control swine flu.

For instance, the directorate of health services in Kerala has issued guidelines asking clinicians to administer oseltamivir to patients in the vulnerable groups – children and the elderly, pregnant women and those with pre-existing medical conditions like diabetes and hypertension – with the onset of symptoms. This is the only drug known to work against H1N1 infections. However, health authorities have found that delays in diagnosis and treatment have been the major factor leading to deaths.

In 15 out of the 40 H1N1 deaths reported in Kerala this year, patients did not receive oseltamivir. Even the remaining 25 patients were given the drug at later stages of the infection. Health authorities found that the delay was a result of the drug being unavailable in private hospitals. “Like all other metros, even in Kerala patients prefer going to private hospitals,” said Dr Reena KJ, Kerala’s nodal officer for infectious diseases. “Doctors were either reluctant to diagnose H1N1 and prescribe the drug or they diagnosed but didn’t have the drugs.”

The state has now ordered all private hospitals to ensure that they have sufficient stocks of oseltamivir.

Everyone is susceptible now

In Gujarat, 33 out of 136 patients with H1N1 have died since the beginning of the year. The largest number of deaths have occurred in Rajkot district, but officials have not been able to assess why this one district has had so many deaths.

“If we don’t know why these people are dying, how can we save them,” said a medical officer from health department of Gujarat.

“All the cases are sporadic,” said a senior Gujarat government official, referring to the fact that the cases and deaths have not been restricted to a particular families or neighbourhoods or communities. “Not a single H1N1 patient is related to another.”

The Gujarat health department has sent swab samples of those who have died of H1N1 to the National Institute of Virology in Pune. They are looking for whether a new H1N1 virus strain, formed from mutations of the old strain, is now circulating.

Genetic changes in influenza viruses occur in two ways. Sometimes, there is an abrupt significant mutation that creates a new strain of virus. The phenomenon is called antigenic shift and can cause dangerous outbreaks like the H1N1 pandemic of 2009. But influenza viruses more often undergo small genetic changes that creates viruses that are only slightly different from the original virus. A person who has been exposed to the original virus may have developed immunity to it but will not be immune to this newer version created by such an antigenic drift.

The National Institute of Virology testing swab samples from Gujarat has reported that the virus seems to have evolved slightly through possible antigenic drift but has not mutated. Despite this, Dr MS Chadha, the influenza group leader at the institute. said that the change “is inconsequential for the clinical severity and transmission of H1N1 virus in circulation in India”.

So far, people whose immunity is already weak or compromised – children and the elderly, pregnant women and those with pre-existing medical conditions like diabetes and hypertension – have been more susceptible to all types of influenzas than others. However, in this year’s outbreak in Maharashtra about 40% of the 215 deaths have been of healthy individuals.

“We don’t have a good reason to explain the deaths in healthy individuals,” said a health official from Maharashtra.

This is another aspect of this year’s outbreak that scientists at the National Institute of Virology are trying to decipher.

Does the flu vaccine work?

Health authorities in both Gujarat and Kerala are in the process of procuring seasonal flu vaccines as per the WHO’s recommendations even though they are not sure about the vaccine’s efficacy.

“[The WHO] predicts the viruses which are likely to be prevalent in northern and southern hemisphere, and accordingly the ingredients of the vaccine are decided,” said Dr Abhay Chaudhary, senior microbiologist from Mumbai.

This year public health experts around the world have called for production of a more comprehensive vaccine than in previous years.

“Hence, the WHO has recommended a vaccine which provides immunity against four type of influenza viruses including H1N1 and its serotype,” said Chaudhary.

Maharashtra has been providing free voluntary influenza vaccine to its healthcare workers, pregnant women, children and those with medical conditions that make them vulnerable. However, a senior health official from the state said: “There are not enough takers of the vaccine.”

If residents across influenza affected states are sceptical about the vaccine, so are health poficials. “The vaccine provides only 60% immunity which means that there is still a possibility of contracting the infection,” Reena of the Kerala health department. “In Kerala, there is a lot of distrust against vaccine and hence we want to focus more on early detection and quick treatment.”

Vaccines have typically been administered before the monsoons because of long-standing observations of influenza outbreaks during and after the rains. Influenza in summer has not been common and the influenza viruses have been considered to be unable to thrive in high temperatures. But, even this seems to be changing.

In 2015, the majority of deaths were recorded in the first week of March. In 2016, most deaths occurred in the first week of February. This year, so far, the largest number of deaths has been in April.

“Ideally, we don’t see H1N1 cases in summer,” said Chaudhary. “We don’t know why India is reporting cases in summer this year. Influenza is common throughout the year but peaks during and after monsoon, which is not the case in India anymore.”

With swine flu striking earlier in the year, the procurement of vaccines seems a step that is too late. “We have started the procurement only after so many people died,” said the senior official from Gujarat. “Till, we get the vaccines, the influenza season will be over.”