The Institute of Advanced Virology at Thonnakkal, Thiruvananthapuram, has acquired PCR testing facility for confirmatory diagnosis of hantavirus infections.
As the appearance of a rare strain of hantavirus with the potential for human-to-human transmission raises global health concerns, in Kerala, virologists and clinicians have been contemplating a critical public health question: What proportion of acute febrile illness with renal syndrome and thrombocytopenia (lowered platelet count) reported in the State, currently attributed to suspected leptospirosis, could actually be due to hantavirus?
The Health department is acutely aware of the fact that hantavirus (the scientific name being Orthohantavirus) could be the new emerging pathogen in the State, given the fact that hantavirus seropositivity (presence of antibodies against hantavirus in blood samples, indicative of infection) has already been reported in Kerala in multiple research studies and as early as 1999.
Serological and clinical evidence of hantavirus infection in India — and in Kerala — was documented in 1999 when 30 serum samples from Kochi were sent to the Laboratory of Clinical and Epidemiological Virology at the University of Leuven, Belgium, to test for hanta. Two cases were found to be hanta positive in the IgM and IgG antibody test. The hanta serotype identified were Seol virus (SEOV) and Puumala virus (PUUV)
The State had also reported one probable case of hantavirus-induced hemorrhagic fever with renal syndrome (HFRS) that mimicked leptospirosis in 2014 but there was no confirmatory diagnosis at the time.
Kerala has a huge annual burden of leptospirosis cases, with farming, sanitation work and monsoon floods driving the spillover of the pathogen from animals to humans. Rodent-borne hantaviruses are also circulating in the same agro-ecological zone, meaning that human exposure to these viruses is plausible.
Two major diseases
The hantavirus is primarily known for causing two major human diseases, hantavirus pulmonary syndrome and HFRS, with the latter being more common in India.
The clinical symptoms of both leptospirosis and hantavirus-induced HFRS — high grade fever with myalgia, lowered platelet count, acute kidney injury and haemorrhagic manifestations — are so similar that these often cannot be distinguished without targeted serology tests.
“Our clinicians are very well aware that one of the differential diagnoses of leptospirosis is hantavirus infection. The theory is that a good number of “leptospirosis-like” illnesses that we see, wherein, patients deteriorate and die within four to five days could be due to hantavirus or a co-infection of both leptospirosis and hanta. These cases often remain documented as ‘unconfirmed/probable leptospirosis’ for lack of timely diagnosis,” says R. Aravind, Head of Infectious Diseases, Government Medical College, Thiruvananthapuram.
Mortality rate of up to 15%
HFRS due to hantaviruses is a serious disease with a reported mortality rate of up to 15% in southeast Asia but no human-to-human transmission has been reported.
“Hantavirus might be a new emerging pathogen for the State, but there is no imminent public health threat. Unlike before, we have diagnostic facilities now at the Institute of Advanced Virology (IAV) and HFRS cases that are leptospirosis-negative are being routinely tested for hantavirus,” Dr. Aravind says.
In one of the latest studies published in December 2025 by Chandy et al, serum samples from 216 febrile patients, presented at Lisie Hospital, Kochi were tested for anti-orthohantavirus IgM and IgG antibodies. In total, 16.2% of the samples were positive for anti-orthohantavirus IgM and 11.57% for IgG antibodies, while both IgM and IgG were detected in 4.63% of the samples, indicating possible virus exposure.
Better access to tests now
Till now, access to both serology tests like IgM Elisa as well as molecular diagnostic tests like PCR for hantavirus has been limited in Kerala as well as across the country. (Serology tests have limitations as detectable levels of antibodies may not show up in the tests in the acute phase of the disease. There are also risks of hantavirus cross-reacting with other viruses, resulting in false negatives).
The IAV has now filled this diagnostic void by acquiring the PCR testing facility for confirmatory diagnosis of hantavirus infections.
“We have never done active surveillance for hantavirus despite serological evidence of the circulation of the virus. We are now routinely doing PCR testing of clinical samples from Thiruvananthapuram MCH for hanta, but so far there have been no positive cases,” says E. Sreekumar, Director of IAV. The IAV has also initiated some basic biological studies on the virus.
Published – May 09, 2026 09:07 pm IST