NIV unable to conduct whole genome sequencing as Zika virus samples not taken during peak viraemia

Scientists from the Indian Council of Medical Research’s (ICMR’s) National Institute of Virology (NIV) Pune are unable to conduct whole genome sequencing on serum samples of Zika virus patients sent by the Pune Municipal Corporation (PMC) as the samples are not taken during peak viraemia, officials said.

The PMC health department had sent 109 blood and urine samples to the NIV. Out of these, as many as 12 people tested positive for Zika virus infection, which includes six pregnant mothers. As most of the samples received by the NIV scientists lacked adequate viral load, the scientists were only able to detect the presence of the virus but it wasn’t enough to sequence the entire genome.

A senior doctor from the PMC, requesting anonymity, said, “Most of the samples that we collected were when the symptoms of the patients had already started to subside. As per the NIV officials, when samples are taken in the late stage of the illness, the patients already have antibodies developed to fight the infection. Samples taken in the later stage and antibodies leave less or inadequate viral load in the serum samples that hardly helps to conduct sequencing.”

According to experts, around 0.3ml of blood serum of an infected patient is enough for whole genome sequencing. The Zika virus-infected patient develops symptoms, most commonly fever, at the end of the incubation period. The patient develops a fever after viraemia, as an immune response to the virus infection. The blood samples if taken during peak viraemia within three days of the infection can help scientists extract the RNA of the virus. This helps in identifying the virus lineage or mutation which may be deleterious to humans.

Dr Rajesh Dighe, assistant health officer of the PMC, said that the NIV scientists have informed them that it becomes difficult to conduct genome sequencing if the samples are taken after three days of peak fever. “Most of the patients that we come across come late to us when the illness has already started to subside. The samples collected by us are not late but the patients come to us in the late stage of the virus. The samples sent by us are of asymptomatic close contact and symptomatic patients,” Dr Dighe said.