As of 2 January, a total of 312 cases of the JN.1 variant have been identified out of 449 samples sent to INSACOG labs since November 2023.
Three out of four cases in December, turned out to be of JN.1 (Shutterstock)
Seven out of ten samples sent by state health authorities for genome sequencing are testing positive for the JN.1 variant of Covid-19, as reported by the Indian SARS-CoV-2 Genomics Consortium (INSACOG).
As of Tuesday, 2 January, a total of 312 cases (69.4 percent) of the JN.1 variant have been identified in India out of 449 samples sent to INSACOG laboratories nationwide since November 2023. In December, three out of four cases were found to be of the JN.1 variant.
Certain states, like Karnataka and Delhi, have mandated genome sequencing for all samples from positive Covid-19 cases as part of their protocol. Here, all samples that yield a positive result for Covid-19 undergo a subsequent stage of genome sequencing.
The World Health Organization (WHO) classified the SARS-CoV-2 subvariant JN.1 as a distinct variant of interest (VOI) from its original lineage BA.2.86 due to its rapid proliferation.
The earliest known case of the JN.1 variant emerged in Kerala on 10 November, when a male patient tested positive for Covid-19, prompting genome sequencing of his samples.
INSACOG’s data shows that in December, 279 Covid-19 cases recorded in the country had the presence of JN.1 out of 368 samples, while 33 such cases were detected in November out of 81 samples.
The JN.1 variant of Covid-19 has been reported in a total of nine states and one Union territory.
In Kerala, 147 out of 204 samples sent to INSACOG-associated labs since November 2023 tested positive for JN.1, accounting for 72 percent of the samples.
Goa reported that 51 out of 56 samples subjected to genome sequencing were positive for JN.1, representing 91 percent of the samples.
Similarly, in Gujarat, 34 out of 50 samples (68 percent) tested positive, while in Maharashtra, 26 out of 44 samples (48 percent) were identified as JN.1 variant positive.
Tamil Nadu recorded 22 out of 30 samples (73 percent) positive for the JN.1 variant, Delhi with 16 out of 20 samples (80 percent), Karnataka with eight out of 18 samples (44 percent), Rajasthan with five out of eight samples (63 percent), Telangana with two out of four samples (50 percent), and Odisha with one positive sample for the JN.1 variant.
In recent months, several states in India have been observing zero Covid-19 cases within their borders. However, since December 2023, there has been a notable surge in Covid-19 cases across the country. As of 2 January, as many as 4,565 active Covid-19 cases across India have been reported.
Among the states affected, Kerala currently has the highest count with 1,712 active cases, followed by Karnataka with 1,245 active cases, Maharashtra with 732 cases, Tamil Nadu with 181 cases, Andhra Pradesh with 119 cases, and Telangana with 50 reported active cases.
Dr. Rajeev Jayadevan, Co-Chairman of the National Indian Medical Association Covid Task Force, stated that India’s INSACOG data from November to December illustrates a significant shift in monthly genomic sequences, emphasising the escalation in Covid-19 cases.
In November, 45 percent of the sequences analysed were identified as the JN.1 variant. However, by December, this proportion surged to 80 percent, nearly doubling within a month’s span.
“This surge in cases can be attributed to two distinct factors: first, the evident rise in Covid-19 cases on the ground, and second, the increase in percentage directly linked to the emergence and prevalence of the new variant, JN.1,” Dr Jayadevan said.
Reflecting on April of the previous year, Dr Jayadevan noted that the majority of sequenced variants were XBB and XBB sublineages. However, the drastic shift to 80 percent JN.1 in December signifies the swift rise of this variant, which is only one mutation away from its predecessor, the relatively benign B.1.2.86 variant.
Despite its initial unassuming nature, B.1.2.86 remained relatively inert, although it possessed numerous mutations previously unseen. However, with a single mutation, particularly in the spike protein, the JN.1 variant rapidly gained momentum, signifying its alarming potential.
“It’s crucial to note that while there are other mutations within the virus, certain changes might indirectly impact its behaviour or actions. However, for the sake of clarity, readers should understand that a single spike mutation, such as L455S, has significantly altered the variant’s characteristics, contributing to its rapid spread and potential implications,” explained Dr Jayadevan.
Despite its ability to rapidly spread, the infection is milder and mostly asymptomatic. Information from across the world suggests that the cases are mild, with symptoms such as a cold, sore throat, low-grade fever (around 100 degrees Fahrenheit), body pain, weakness, and dry cough.
People are recovering quickly as these symptoms are generally manageable with symptomatic treatments like fever-reducing medication and pain relief.
While the WHO has classified JN.1 as a separate “variant of interest” due to its rapidly increasing spread, it poses a “low” global public health risk.
The Indian Medical Association (IMA) in Telangana conducted a survey amongst a small cohort of doctors, which included a paediatrician, pulmonologist, and general physician from across Telangana. The survey was conducted to determine the kinds of cases visiting the hospital after the reported increase in Covid-19 cases.
“Our survey included over 20 doctors encompassing various specialties, such as physicians and paediatricians. The majority of these professionals indicated that approximately 10 to 25 percent of their cases were related to respiratory issues. Within this range, most patients exhibited mild to moderate symptoms, regardless of whether they were paediatric or older individuals. Remarkably, around 98 percent of these cases did not necessitate hospitalisation,” said IMA Telangana spokesperson Dr Kiran Madala.
He added that a very small percentage, less than 1 to 2 percent, required admission to a hospital due to the severity of their condition.
Consequently, there seems to be little cause for alarm, as this pattern is not isolated and has already permeated the community, including at the district level.
“It’s noteworthy that the majority of patients, including children, do not require hospitalisation based on the insights gathered from our survey conducted within the community,” said Dr Madala.
“The encouraging aspect here is that the majority of cases can be managed effectively with simple treatments. However, the current governmental approach needs a shift; instead of emphasising increased testing, there should be a call for Severe Acute Respiratory Infection (SARI) surveillance,” said Dr Madala.
This entails a proactive approach, possibly through door-to-door surveys conducted by Auxiliary Nurse Midwives (ANMs) to identify individuals suffering from any form of respiratory sickness, be it tuberculosis or Covid. Once identified, these individuals can be directed to the hospital for proper treatment.
“This approach prioritises identifying and assisting those who are already at risk, rather than merely escalating testing efforts. By providing timely treatment to those in need, we can potentially save lives,” he said.
Dr Jayadevan said that the current scenario with Covid-19 presents a complex picture. Despite its widespread prevalence, many individuals exhibit either mild symptoms or no symptoms at all, resulting in a lower likelihood of hospitalisation. Hospital data systems do not indicate overwhelming strain due to Covid-19 cases.
“However, there’s an additional factor to consider: the presence of other viruses like influenza. Unlike the situation in 2020-2022, 2023 witnessed the resurgence of various viruses like adenovirus, rhinovirus, and others. These viruses have resurfaced for several reasons, including the reduced exposure and natural immunity due to lockdowns and social distancing measures.,” Dr Jayadevan said.
He added, “This resurgence is often misinterpreted as Covid-19 causing immunosuppression when, in reality, it’s a consequence of increased susceptibility among individuals who haven’t encountered these viruses in recent years.”
Dr Jayadevan added that influenza, for instance, behaves differently and isn’t tied to a specific season in India as it is in the West. It lingers for a few months and can manifest in various strains like influenza A, predominantly H1N1 or H3N2. The coexistence of Covid-19 and influenza complicates diagnoses in healthcare settings.
“Healthcare facilities aren’t overwhelmed in terms of patient admissions or ICU occupancy. Still, some individuals, particularly older adults or those with underlying health conditions like kidney or liver diseases, have unfortunately succumbed to Covid-19. However, these cases aren’t numerous,” he stated.
The actual number of Covid-19 tests conducted remains lower than perceived, contributing to underreported figures. Some hospitals reserve tests for severe cases or primarily focus on bacterial pneumonia diagnosis, neglecting Covid-19 testing in less severe cases. Consequently, deaths that could be linked to Covid-19 might not be diagnosed or reported as such, leading to an underestimation of Covid-19 cases.
For instance, a patient known for conditions like asthma or heart failure might be admitted due to heart failure, and Covid-19 testing might not occur. If such a patient eventually succumbs to heart failure, even if Covid-19 was a contributing factor, it might not be recorded as a Covid-19-related death.
As Covid-19 cases increase across the country, Bengaluru is witnessing a wave-like situation as noted by wastewater surveillance.
The positivity rate of SARS-CoV-2 from the samples collected from the wastewater in Bengaluru city between 11 and 29 December 2023 was around 96 percent. These samples were collected across 26 sewage treatment plants (STP).
Wastewater surveillance of viruses has been done by the Tata Institute of Genetics and Society (TIGS), Bengaluru, in collaboration with the BBMP.
The surveillance shows the viral load of SARS-CoV-2 in the wastewater that comes from the households of the community. For more information about how it works, read here.
Between 10 and 15 December, the SARS-CoV-2 copies per ml were 2,000, now it has increased to more than 3,000 copies per ml. In some areas near Yele Mallappa Shetty Lake STP in East Bengaluru, the SARS-CoV-2 viral load is more than 30,000 copies per ml, TIGS reported.
#Realtime #SARSCoV2 viral load in sewershed sites #wastewaters and reported #COVID-19 cases – the viral load shows an increase and mainly driven by #JN.1 variant and its sublineages.
There is no clinical testing data available since 8th Nov. pic.twitter.com/YEJOEf3shM
— Tata Institute for Genetics and Society, India (@TIGS_India) January 1, 2024
“This indicates a rise in the viral load within wastewater, signifying an increasing number of individuals shedding the virus. The current substantial data reveals a persistent upward trend, dispelling any initial concerns of a false alarm,” Dr Rakesh Mishra, Director of TIGS, told South First.
He added that the trend remains consistent, approximately 1.5 times the previous pattern, indicating a continued increase in the number of people shedding the virus. This phenomenon is observed not only in Bengaluru but also in other locations, such as Hyderabad, and potentially across the country due to extensive travel via air and train, creating a rapid homogeneity.
May 15, 2024
May 15, 2024
May 15, 2024
May 15, 2024
May 15, 2024
May 15, 2024
