Appearance and Prevalence of JN.1 SARS-CoV-2 Variant in India and Its Clinical Profile in the State of Maharashtra

Abstract

Background: In August 2023, the BA.2.86 SARS-CoV-2 variant, with over 30 spike protein mutations, emerged amidst the global dominance of XBB sub-lineages. It evolved into JN.1 by late 2023, spreading across 71 countries. JN.1, distinct for its L455S mutation, significantly dominated global sequences, raising concerns over its transmission and clinical impact. The study investigates JN.1's clinical severity and its effect on hospital admissions in Maharashtra, India.

Methodology: The present study involved 3,150 curated Indian SARS-CoV-2 whole genome sequences with collection dates between 1st August 2023 and 15th January 2024. Lineage and phylogenetic analysis of sequences was performed using Nextclade. Telephonic interviews were conducted to confirm the demographic details and obtain clinical information on the JN.1* (* indicates JN.1 and all its sub-lineages) cases. The obtained data were recorded and analyzed using Microsoft® Excel (Microsoft Corporation, Redmond, WA).

Results: Out of 3,150 sequences analyzed, JN.1* was the most common lineage (2377/3150, 75.46%), followed by XBB.2.3* (281/3150, 8.92%) and XBB.1.16* (187/3150, 5.94%). In India, it was first identified on 6th October 2023, in Kerala. The highest proportion of JN.1* sequences originated from Maharashtra (628/2377, 26.42%), followed by West Bengal (320/2377, 13.46%), Andhra Pradesh (293/2377, 12.33%), Kerala (288/2377, 12.12%), and Karnataka (285/2377, 11.99%). In Maharashtra, the JN.1* variant was first identified on 23rd November 2023. A total of 279 JN.1* cases were included in the clinical study. Of these, 95.34% (266/279) had symptomatic disease with mild symptoms; cold (187/279, 67.03%) being the most common symptom, followed by fever (156/279, 55.91%), cough (114/279, 40.86%), and headache (28/279, 15.64%). Of all the cases, 13.26% (37/279) required institutional quarantine or hospitalization, and the rest were isolated at home. Among the hospitalized patients, 54.05% (20/37) cases were given conservative treatment while 45.95% (17/37) cases required supplemental oxygen therapy. Regarding the vaccination status, 94.26% (263/279) of cases received at least one dose of the COVID-19 vaccine, while 5.02% (14/279) were not vaccinated, of which most were children aged zero to nine years (5/14, 35.71%). The overall recovery rate among JN.1* cases was 98.57% (275/279), with 1.43% (4/279) cases succumbing to the disease.

Conclusion: The JN.1* variant, the dominant variant in India, exhibits clinical features similar to previous circulating variants in Maharashtra without increased severity. Its notable transmissibility underscores the importance of studying the ongoing viral evolution. The pressing necessity for swift identification and the clinical features of new variants is essential for effective public health response.

Introduction

At the time when the sub-lineages of the recombinant SARS-CoV-2 variant, XBB, were predominant globally, a new sub-lineage of BA.2 appeared around August 2023 [1]. This new lineage of SARS-CoV-2 was labeled as BA.2.86 on 17th August 2023 [2]. BA.2.86 had more than 30 spike (S) protein mutations over and above its parent lineage, BA.2 [1]. It was first sequenced in Israel and reported on 13th August 2023 [3]. Alarmed by its potential to evade pre-existing immunity against SARS-CoV-2 developed by the administration of vaccines and from previous infections, the World Health Organization (WHO), within four days, promptly designated it as a variant under monitoring (VUM) on 17th August 2023, the day it was labeled as BA.2.86. Later, due to its growing prevalence, as evidenced by genomic surveillance, the WHO escalated its status to the variant of interest (VoI) on 21st November 2023 [4].

In late 2023, the BA.2.86 SARS-CoV-2 variant evolved, leading to the emergence of the JN.1 (BA.2.86.1.1) variant. It was first identified in the United States in September 2023 [5]. At the same time, it was identified in 12 more countries, with the highest proportions in Canada, France, Singapore, Sweden, the United Kingdom, and the United States [6]. Initially monitored within the BA.2.86 variant, the rapid and extensive spread of JN.1 across various nations prompted WHO to designate it as a VOI on 20th December 2023, thereby acknowledging its distinction from its parent lineage, BA.2.86. According to the WHO reports as of 19th January 2024, JN.1 has emerged as the most reported VOI globally, with detection in 71 countries and accounting for 65.5% of all sequences in the final week of 2023 [7]. By January 2024, the JN.1* variant dominated India, representing 97.25% of Indian sequences on the Global Initiative on Sharing All Influenza Data (GISAID), thus highlighting the significant impact and global concern over its transmission dynamics [8].

While JN.1 is closely related to its precursor, BA.2.86, it features a unique mutation, L455S, in the receptor-binding domain (RBD) of its spike protein, alongside three additional mutations in non-spike proteins. A similar L455F mutation in variants HK.3 and other FLip variants has been shown to enhance transmissibility and immune evasion compared to the original EG.5.1 variant [9]. However, information is scarce regarding the potential impact of JN.1 on clinical outcomes. Therefore, the current study aims to evaluate the clinical severity associated with JN.1 infections and its implications for hospital admissions in Maharashtra.

Materials and methods

The present study is a part of the sequencing activity in Maharashtra under the Indian SARS-CoV-2 Genomics Consortium (INSACOG) to study the evolutionary patterns and epidemiological characteristics of SARS-CoV-2.

SARS-CoV-2 whole genome sequences in India: lineage and phylogenetic analysis

To trace the first appearance and the spread of the JN.1 SARS-CoV-2 variant in India, whole genome sequences of the virus, with sample collection dates from 1st August 2023 to 15th January 2024, submitted by various sequencing laboratories in different states and Union Territories of the country, were downloaded from the Indian Biological Data Centre (IBDC) database [10] with their kind permission. Entries with complete metadata, including geographic locations and sample collection dates, were included in the study and the sequences used are accessible in the supplemental table in the Appendices. The lineage and clade analysis were performed using Nextclade software (version 3.0.1). The phylogenetic tree was constructed using Nextclade Augur and visualized using Auspice (version 2.52.1).

Demographic and clinical data collection of SARS-CoV-2-positive cases in Maharashtra

Demographic details, including age, sex, area of residence, contact number, and date of sample collection and testing, were collected from the metadata provided to the sequencing laboratories by the reverse transcription-polymerase chain reaction (RT-PCR) testing centers. Telephonic interviews were conducted with each patient to confirm their demographic details and obtain clinical information such as symptoms, isolation type, hospitalization, oxygen requirements, treatments, and vaccination status. Those patients who chose not to disclose their clinical history during the interview were documented and excluded from the study.

Also, daily records from 1st August 2023 to 15th January 2024 were collected from the State's District Health Services Department to assess the severity of illness linked to the JN.1 SARS-CoV-2 variant during its surge in Maharashtra and its impact on public health. The data collected included the daily total number of samples tested for SARS-CoV-2, test positivity, hospital admissions, and the demand for oxygen throughout the state.

Statistical analysis

All demographic and clinical data were recorded and analyzed using Microsoft® Excel (Microsoft Corporation, Redmond, WA), and analysis was performed using Microsoft® Excel. Continuous variables were presented as median and interquartile range (IQR). Categorical variables were presented as numbers and percentages.

Results

Distribution of SARS-CoV-2 lineages in India

A total of 3,150 downloaded sequences were included in the study following data curation. A total of 144 different lineages were identified following Nextclade Pangolin nomenclature. JN.1* was the most common lineage (75.46%), followed by XBB.2.3* (8.92%) and XBB.1.16* (5.94%) (Table 1).

Table 1. Distribution of SARS-CoV-2 variants among sequences deposited on IBDC from India.

IBDC: Indian Biological Data Centre.

Clade	Nextclade Pangolin lineage		Count (%)
21K	BA.1*	BA.1	2	23 (0.73%)
		BA.1.1	21
21L	BA.2*	BA.2	31	56 (1.78%)
		BA.2.1	4
		BA.2.10.4	1
		BA.2.12	1
		BA.2.38	13
		BA.2.38.1	1
		BA.2.76	1
22C		BA.2.12.1	1
		CH.1.1.24	1
		DV.7.1.3	1
		FK.1.1	1
22B	BA.5*	BA.5	1	5 (0.16%)
		BA.5.5	1
		BA.5.5.1	1
		BE.1.1	1
22E		BQ.1.22	1
23A	XBB.1.5*	GF.1	1	11 (0.35%)
		JD.1.1	2
		XBB.1.5	6
		XBB.1.5.28	1
23G		GK.1.1	1
23D	XBB.1.9*	XBB.1.9.1	2	47 (1.49%)
		EG.5.2	1
		FL.1.5	1
		FL.1.5.1	2
		FL.13.2	1
		FL.13.4.1	1
		FL.4.8	1
		HN.5	1
23F		EG.5.1	3
		EG.5.1.1	5
		EG.5.1.15	1
		EG.5.1.3	1
		EG.5.1.6	2
		EG.5.1.8	1
		HK.19	1
		HK.29	1
		HV.1	10
		HV.1.11	2
		JG.3	3
		JG.3.2	1
23H		HK.3	4
		HK.3.1	1
		HK.3.5	1
23B	XBB.1.16*	XBB.1.16	57	187 (5.94%)
		XBB.1.16.1	17
		XBB.1.16.11	37
		XBB.1.16.12	3
		XBB.1.16.13	1
		XBB.1.16.17	32
		XBB.1.16.18	3
		XBB.1.16.2	1
		XBB.1.16.24	28
		XBB.1.16.8	1
		FU.1	3
		FU.3.1	1
		JF.1.1	1
		JM.2	2
23E	XBB.2.3*	GE.1	85	281 (8.92%)
		GE.1.1	10
		GJ.1	4
		GJ.1.1	8
		GJ.1.2	2
		GJ.3	1
		GJ.6	4
		GS.1	1
		GZ.1	5
		HH.1	1
		HH.2	5
		HH.6	10
		HH.8	1
		JE.1	1
		JY.1	44
		JY.1.1	47
		XBB.2.3	15
		XBB.2.3.10	1
		XBB.2.3.11	2
		XBB.2.3.12	1
		XBB.2.3.18	1
		XBB.2.3.19	2
		XBB.2.3.2	7
		XBB.2.3.22	1
		XBB.2.3.3	20
		XBB.2.3.5	1
		XBB.2.3.8	1
23I	BA.2.86*	BA.2.86	15	32 (1.02%)
		BA.2.86.1	12
		JN.2	3
		JN.4	1
		JN.6	1
	JN.1*	JN.1	1026	2377 (75.46%)
		JN.1.1	959
		JN.1.1.1	1
		JN.1.1.3	1
		JN.1.10	7
		JN.1.11	304
		JN.1.2	2
		JN.1.3	2
		JN.1.4	36
		JN.1.5	21
		JN.1.6	1
		JN.1.7	1
		JN.1.8	10
		JN.1.9	6
22F	Other XBBs	XBB	1	13 (0.41%)
		XBB.1	1
		GW.5.1.1	3
		GW.5.3.1	2
		JC.2	2
		KE.2	1
		XBB.1.41.1	1
		XBB.2.4	1
		XBB.2.6	1
Recombinant	Other recombinant variants	XAC	1	35 (1.11%)
		XAD	2
		XAF	1
		XAG	2
		XAH	2
		XAK	1
		XBH	1
		XBQ	1
		XBW	1
		XCG	1
		XCH.1	1
		XDA	12
		XDA.1	1
		XDB	3
		XDD	4
		XDK	1
19A	Other lineages	B	4	44 (1.40%)
20A		B.1	7
20B		B.1.1	11
		B.1.1.161	4
		B.1.1.220	1
		B.1.1.519	2
20C		B.1.566	1
20F		D.2	1
20G		B.1.2	2
21C		B.1.429	3
21J		AY.4	2
21M		B.1.1.529	5
22A		BA.4.6	1
Lineage unassigned (due to poor quality sequences)			39 (1.24%)
Grand total			3150

Figure 1 illustrates the evolutionary relationship of the JN.1* variant (clade 23I) in comparison to other variants. In India, the temporal distribution of variants indicates that the XBB variant and its related lineages were predominant from week 31, 2023, until week 45, 2023 (Figure 2). The JN.1* variant was first identified in Indian sequences on 6th October 2023 in Kerala. Subsequently, by December 2023, the JN.1* variant became the most prevalent variant across India. The JN.1* variant has grown from 8.33% since its first detection in week 40, 2023, to 93.83% in week two, 2024. Of all the sequences submitted by various states, 75% are of the JN.1* variant, with the highest proportion of JN.1* sequences originating from Maharashtra (26.42%), followed by West Bengal (13.46%), Andhra Pradesh (12.33%), Kerala (12.12%), and Karnataka (11.99%) (Figure 3).

Figure 1. Evolutionary relationship of clade 23I with other clades in India.

The figure represents the phylogenetic relationship of clade 23I with other clades identified in Indian sequences during the study period. The horizontal axis of the phylogenetic tree denotes the number of mutations, with the numbers increasing progressively from left to right. The branches, represented by horizontal lines, signify evolutionary divergence over time. The length of the branch horizontally correlates with the amount of change. The vertical axis on the other hand organizes the clade labels in a spatial manner for clarity. It does not imply any phylogenetic or temporal relationship.

Image credits: Rashmita Das

Figure 2. Temporal distribution of SARS-CoV-2 variants based on sequences submitted to the IBDC in India.

IBDC: Indian Biological Data Centre.

Image credits: Rashmita Das

Figure 3. Geographic distribution of the 2377 JN.1* SARS-CoV-2 sequences based on sequences submitted to the IBDC in India.

IBDC: Indian Biological Data Centre.

Image credits: Rashmita Das

Test positivity and lineage distribution of SARS-CoV-2 in Maharashtra

Figure 4 represents the overview of SARS-CoV-2 testing in Maharashtra, tracking the total number of tests performed (including RT-PCR and antigen testing) and the positivity rate from the 31st week of 2023 through the second week of 2024. The total tests performed show significant variability with notable spikes toward the end of the period (in weeks 52 of 2023 and the first and second weeks of 2024), suggesting increased testing efforts during these weeks. Similarly, the weekly positivity rate also experienced fluctuations throughout the period. The highest positivity rate was 2.67% in the 38th week of 2023. Following this peak, the positivity rate gradually declined, reaching its lowest in the 45th week (0.21%) and increasing again to 1.81% in the 51st week. Following the first detection of the JN.1* variant globally, the testing efforts in the state and the country were increased [11], thus explaining the variations in both the number of tests performed and the positivity rate reflecting the changes in the testing strategies and the public health policies in the state.

Figure 4. Weekly tests performed versus weekly count of positive cases in Maharashtra between 1st August 2023 and 15th January 2024.

Image credits: Rashmita Das

Figure 5 presents the weekly distribution of SARS-CoV-2 variants in Maharashtra from week 31, 2023 to week two, 2024, mirroring the trend observed across India. The JN.1* variant was first identified on 23rd November 2023, and its prevalence rose from 20% in week 47, 2023, to 100% by the second week of 2024.

Figure 5. Temporal distribution of SARS-CoV-2 variants based on sequences submitted to the IBDC from Maharashtra.

IBDC: Indian Biological Data Centre.

Image credits: Rashmita Das

Demographic and clinical characteristics of JN.1* SARS-CoV-2 variant in Maharashtra

Out of 628 JN.1* cases in Maharashtra, 550 (87.58%) cases had complete metadata available and were included in the demographic study (Table 2). Of these 550 participants, 55.45% were males and 44.55% were females. The median age of the study population was 42 (IQR: 30-60) years, with individuals aged 60 years and above (25.09%) being predominantly affected.

Table 2. Demographic characteristics of JN.1* SARS-CoV-2 variant in Maharashtra (n = 550).

Demographic characteristics	Count (%)
Gender-wise distribution
Male	305 (55.45%)
Female	245 (44.55%)
Age-wise distribution (in years)
0-9	05 (0.91%)
10-19	39 (7.09%)
20-29	84 (15.27%)
30-39	115 (20.91%)
40-49	84 (15.27%)
50-59	85 (15.45%)
60 and above	138 (25.09%)
Area-wise distribution
Ahmednagar	02 (0.36%)
Akola	02 (0.36%)
Amravati	18 (3.27%)
Chhatrapati Sambhajinagar	54 (9.82%)
Beed	03 (0.55%)
Bhandara	01 (0.18%)
Hingoli	03 (0.55%)
Jalgaon	04 (0.73%)
Jalna	02 (0.36%)
Kolhapur	10 (1.82%)
Mumbai	18 (3.27%)
Nagpur	36 (6.55%)
Nanded	02 (0.36%)
Nandurbar	01 (0.18%)
Nashik	02 (0.36%)
Osmanabad	02 (0.36%)
Pune	273 (49.64%)
Raigad	18 (3.27%)
Sangli	01 (0.18%)
Satara	01 (0.18%)
Solapur	13 (2.36%)
Thane	83 (15.09%)
Yavatmal	01 (0.18%)

From this subset of 550 cases, attempts to contact 253 (46%) participants were unsuccessful due to non-response to calls, and 18 (3.27%) participants declined participation in the study. Therefore, 279 (50.73%) participants were successfully contacted and included in the clinical study. Table 3 summarizes the clinical characteristics, vaccination status, and outcome of JN.1* cases in Maharashtra. Most JN.1* cases had symptomatic disease (95.34%) with mild symptoms. The most common symptoms were cold (67.03%), fever (55.91%), cough (40.86%), headache (15.64%), body ache (9.68%), and fatigue (8.60%). Underlying comorbid conditions, either alone or in combination, were reported in 17.56% (49 out of 279) of cases, with diabetes mellitus (29, alone or in combination; 59.18%), hypertension (22, alone or in combination; 44.90%), and underlying lung pathology (six, alone or in combination; 12.25%) being the most common conditions.

Table 3. Clinical characteristics of JN.1* SARS-CoV-2 variant in Maharashtra (n = 279).

Out of 550 JN.1* cases with complete metadata, 279 participants were successfully contacted and included in the clinical study.

Clinical characteristics	Count (%)
1. History of previous infection
Present	41 (14.69%)
Absent	238 (85.31%)
2. Presence of comorbidities
a. Present	49 (17.56%)
i. Diabetes mellitus (DM)	18 (36.73%)
ii. Hypertension (HTN)	12 (24.29%)
iii. Underlying lung disease	04 (8.16%)
iv. Arthritis	01 (2.04%)
v. Tuberculosis	01 (2.04%)
vi. Hypothyroidism	01 (2.04%)
vii. Coronary heart disease (CHD)	01 (2.04%)
viii. HIV/AIDS	01 (2.04%)
ix. DM + HTN	08 (16.33%)
x. DM + underlying lung disease	01 (2.04%)
xi. DM + HTN + CHD	01 (2.04%)
xii. DM + HTN + underlying lung disease	01 (2.04%)
b. Absent	230 (82.44%)
3. Vaccination status
a. Vaccinated	263 (94.26%)
i. One dose	12 (4.56%)
ii. Two doses	151 (57.42%)
iii. Booster dose (precautionary dose)	100 (38.02%)
b. Not vaccinated	14 (5.02%)
c. Data not available	02 (0.72%)
4. Symptom status
a. Symptomatic	266 (95.34%)
b. Asymptomatic	13 (4.66%)
5. Presenting symptoms
a. Fever	156 (55.91%)
b. Cold	187 (67.03%)
c. Cough	114 (40.86%)
d. Breathlessness	15 (5.38%)
e. Headache	28 (15.64%)
f. Fatigue	24 (8.60%)
g. Body ache	27 (9.68%)
h. Diarrhea	02 (0.72%)
i. Sore throat	16 (5.74%)
j. Vomiting	02 (0.72%)
k. Chest pain	01 (0.36%)
l. Loss of taste and smell	01 (0.36%)
m. Joint pain	01 (0.36%)
6. Type of quarantine
a. Home isolation	242 (86.74%)
b. Hospital isolation/hospitalization	37 (13.26%)
7. Treatment
a. Received no treatment	03 (1.075%)
b. Received symptomatic treatment	259 (92.83%)
c. Received oxygen therapy	14 (5.02%)
i. Non-invasive ventilation	09 (64.29%)
ii. Invasive ventilation	05 (35.71%)
d. Received antiviral/steroid with oxygen	03 (1.075%)
8. Outcome
a. Alive	275 (98.57%)
b. Dead	04 (1.43%)

Regarding the vaccination status, 94.26% (263 out of 279) of cases received at least one dose of the COVID-19 vaccine, while 5.02% (14 out of 279) were not vaccinated. Most unvaccinated individuals were children aged zero to nine years (five out of 14, 35.71%) and adults aged 30-39 years (three out of 14, 21.43%). Covishield (ChAdOx1nCoV-19 coronavirus vaccine) (242 out of 263, 92.01%) was the predominant vaccine administered, followed by Covaxin^TM (BBV152A-a whole inactivated virus-based COVID-19 vaccine) (18 out of 263, 6.84%).

Of all the cases, 13.26% (37 out of 279) required institutional quarantine or hospitalization. Nearly all of the patients who were home-isolated received conservative treatment (240 out of 242, 99.17%), whereas hospitalized patients often received conservative care (20 out of 37, 54.05%) or required supplemental oxygen therapy (17 out of 37, 45.95%). The recovery rate was high; out of 279 cases, 98.57% of cases (275 out of 279) recovered from the disease, while 1.43% (four out of 279) succumbed.

Among the deceased, three were over 60 years of age (75%), and one (25%) was in the age group of 30-39 years. Three out of four cases (75%) suffered from respiratory symptoms and had underlying comorbidities, while one (25%) did not have respiratory symptoms and was admitted to the hospital due to paralysis. Of the three cases with respiratory symptoms, two were aged over 60 years with pre-existing conditions such as chronic obstructive pulmonary disease in one, and diabetes mellitus and hypertension in the other. The third was an immunocompromised individual with HIV/AIDS. Regarding vaccination, two were vaccinated with two doses, one received three doses of vaccine, and the vaccination status was unclear in one.

Weekly trends in isolation bed occupancy in hospitals, oxygen/ventilator support, and COVID-19-positive cases in Maharashtra

Out of the total positive cases in the state, 8.03% (338 out of 4211) required hospital admission. Among these hospitalized cases, 61.24% (207 out of 338) were managed in isolation beds without the need for oxygen support, while the remaining 38.76% (131 out of 338) needed oxygen or ventilator support. Mirroring the state's positivity rate trend, the patterns of hospital admissions and the need for oxygen support also showed fluctuations during the same timeframe (Figure 6).

Figure 6. Weekly trends in isolation bed occupancy in hospitals, oxygen/ventilator support, and COVID-19-positive cases in Maharashtra.

Image credits: Rashmita Das

Discussion

Although the BA.2.86 variant was first reported in August 2023 globally, it did not exhibit significant growth advantages or abilities to evade the humoral immune response compared to the global dominant variants such as EG.5.1 and HK.3 [12]. Over four weeks, from week 40 to week 44 of 2023, the percentage of BA.2.86 sequences slowly and steadily increased from 1.8% to 8.9% [4]. Conversely, the JN.1 variant, distinguished by a single additional mutation (L455S) in its spike protein compared to BA.2.86, swiftly ascended to global dominance. Within the same duration of four weeks, from week 44 to week 48 of 2023, its global prevalence surged from 3.3% to 27.1% [13], making up 95% of all sequences collected globally in February 2024 [14]. The quick shift from XBB sub-lineages to JN.1* mirrors the transition of Delta to the Omicron variant. In the Omicron wave, Omicron's prevalence increased from under 0.1% to 89.1%, making it the globally dominant variant within nine weeks [15,16]. The rapid emergence and dominance of the JN.1 variant in India and globally can be attributed to its enhanced transmissibility due to spike mutation L455S. In the early stages of its emergence, analysis of JN.1's effective reproductive number (Ro) using sequences from France, the United Kingdom, and Spain indicated that the JN.1 Ro exceeded that of both BA.2.86.1 and HK.3, with the latter being among the XBB lineages with the most significant growth advantage as of late November 2023. This analysis predicted JN.1's trajectory toward global dominance, a status that it had achieved in France and Spain by the close of November 2023 [9]. Presently, the JN.1* variant exhibits a relative growth advantage of 57% (confidence interval: 56-57%) [17].

The in vitro angiotensin-converting enzyme 2 (ACE2)-binding assay [9] and surface plasmon resonance analysis [12] using the RBD (monomeric) of JN.1 and BA.2.86 showed a significant reduction in the affinity of the JN.1 RBD when compared to the BA.2.86 RBD for human ACE2 receptor. Conversely, the pseudovirus assay using trimerized whole spike protein showed that the infectivity rate of JN.1 was substantially greater than that of BA.2.86 [9]. The neutralization assays demonstrated a superior ability of the JN.1 variant to evade the immune response compared to BA.2.86, with a 2.1-fold decrease in neutralization titers against antibodies from individuals reinfected with XBB after BA.5/BF.7 infection, and a 1.1-fold reduction from those with XBB breakthrough infections [9,12]. It was also shown that a small change in the L455, which is predominantly located at the epitope of RBD class 1 antibodies, enhanced JN.1's ability to evade class 1 monoclonal antibodies, making up for the fact that the parent variant, BA.2.86, was susceptible to this antibody group. However, one of the therapeutic antibodies, SA55, was shown to retain its efficacy against JN.1 [12]. As indicated by the pseudovirus assay and neutralization assays mentioned earlier, JN.1 has increased infectivity and immune evasion capabilities compared to BA.2.86.

The JN.1 variant caused mild infections in Maharashtra, mirroring the clinical outcomes observed during the previous waves in the state caused by BA.2.75, XBB, and XBB.1.16, with similar rates of hospital admissions, oxygen requirements, and mortality. In contrast to earlier waves where individuals aged 21-40 years were primarily affected, the current wave has seen a significant shift, with those aged 60 years and above being predominantly affected [18-20]. Despite a notable increase in number of positive cases, health services data showed that the overall hospitalization rate during the study period was 8.03%, and oxygen support was needed in 3.11% of positive cases, reiterating our observations that the uptick in case positivity did not significantly impact the hospitalization or oxygen demand in the state.

This evolutionary pattern of JN.1 arising from BA.2.86 is similar to the previous transition of CH.1.1 (BA.2.75.3.4.1.1.1.1) arising from BA.2.75 [12]. Albeit the addition of a new mutation in JN.1 helped it to overcome the competition faced by the parent BA.2.86 from the existing dominant XBB variants. On the other hand, mutations of CH.1.1 helped to evade the neutralizing antibodies developed in the hosts against the parent lineage, i.e., BA.2.75, which had caused widespread infection in the community. The emergence of XBB due to recombination of BJ.1 (BA.2.10.1) and BM.1.1.1 (BA.2.75.3.1.1.1) also demonstrates the innovative evolutionary strategy of SARS-CoV-2 to evade the existing neutralizing antibodies against the parent lineages. This highlights the importance of closely monitoring variants with high ACE2-binding affinity and distinct antigenic characteristics. Hence, the early detection of these mutations is crucial before they lead to evident health implications, a task that case-based surveillance might not adequately accomplish. Instead, implementing broad, population-level surveillance methods, like wastewater-based surveillance, is essential for uncovering cryptic mutations and variants. For instance, a study in Berlin, Germany, demonstrated the effectiveness of this approach by identifying the JN.1 variant in wastewater three weeks before it was detected in clinical samples, highlighting the value of population-based surveillance in early detection efforts [21]. Therefore, prompt identification of novel SARS-CoV-2 variants is vital for facilitating rapid risk evaluations, timely dissemination of information, and coordinated public health responses.

The study suffers from a few limitations. First, the analysis depends on individuals who tested for COVID-19, allowing their samples to be sequenced, and individuals who responded and consented to the study, suggesting that the reported figures might not represent the actual burden of the disease. Secondly, the study is region-specific, with data from Maharashtra. Therefore, the findings of this study might restrict its generalizability to other geographic areas and populations with different demographic characteristics. Additionally, the clinical data were obtained through telephonic conversation, potentially leading to recall bias among patients. Therefore, more comprehensive studies are needed to enhance representativeness and accuracy, including studies in diverse geographic locations and populations and using a wider range of data collection methods.

Conclusions

The JN.1* variant has emerged as the predominant SARS-CoV-2 variant in India, with clinical presentation similar to previous variants circulating in Maharashtra, India. Notably, while JN.1* has not been associated with more severe disease outcomes, its enhanced transmissibility underscores the importance of studying the ongoing viral evolution. The evolution of the virus by adding novel mutations necessitates prompt detection strategies to prevent potential surges. The pressing necessity for swift identification and the clinical features of new variants will enable public health authorities to predict and mitigate the risks effectively, ensuring preparedness against future outbreaks.

Appendices

Table 4. IDs of the sequences used in the study, downloaded from the Indian Biological Data Centre (IBDC), Regional Centre for Biotechnology, Department of Biotechnology, Ministry of Science and Technology, Government of India, with their kind permission.

IDs of the sequences used in the study, downloaded from the Indian Biological Data Centre (IBDC), Regional Centre for Biotechnology, Department of Biotechnology, Ministry of Science and Technology, Government of India, with their kind permission

INCOV286977

INCOV286992

INCOV287059

INCOV287062

INCOV287064

INCOV287066

INCOV287067

INCOV287068

INCOV287069

INCOV287083

INCOV287086

INCOV287087

INCOV287106

INCOV287107

INCOV287108

INCOV287109

INCOV287110

INCOV287111

INCOV287112

INCOV287113

INCOV287117

INCOV287118

INCOV287119

INCOV287121

INCOV287123

INCOV287124

INCOV287125

INCOV287126

INCOV287127

INCOV287129

INCOV287137

INCOV287138

INCOV287140

INCOV287141

INCOV287146

INCOV287147

INCOV287167

INCOV287168

INCOV287169

INCOV287170

INCOV287171

INCOV287172

INCOV287173

INCOV287174

INCOV287175

INCOV287176

INCOV287177

INCOV287178

INCOV287179

INCOV287180

INCOV287181

INCOV287182

INCOV287183

INCOV287184

INCOV287186

INCOV287187

INCOV287188

INCOV287189

INCOV287190

INCOV287191

INCOV287192

INCOV287193

INCOV287194

INCOV287195

INCOV287196

INCOV287197

INCOV287198

INCOV287199

INCOV287200

INCOV287201

INCOV287202

INCOV287203

INCOV287204

INCOV287205

INCOV287206

INCOV287207

INCOV287208

INCOV287209

INCOV287210

INCOV287211

INCOV287212

INCOV287213

INCOV287214

INCOV287215

INCOV287216

INCOV287217

INCOV287218

INCOV287219

INCOV287220

INCOV287221

INCOV287222

INCOV287223

INCOV287224

INCOV287225

INCOV287226

INCOV287227

INCOV287228

INCOV287229

INCOV287230

INCOV287231

INCOV287232

INCOV287233

INCOV287234

INCOV287235

INCOV287236

INCOV287237

INCOV287238

INCOV287239

INCOV287240

INCOV287241

INCOV287242

INCOV287243

INCOV287244

INCOV287245

INCOV287246

INCOV287247

INCOV287248

INCOV287249

INCOV287250

INCOV287251

INCOV287252

INCOV287253

INCOV287257

INCOV287258

INCOV287265

INCOV287266

INCOV287267

INCOV287268

INCOV287269

INCOV287270

INCOV287271

INCOV287272

INCOV287273

INCOV287274

INCOV287275

INCOV287277

INCOV287278

INCOV287279

INCOV287280

INCOV287281

INCOV287282

INCOV287283

INCOV287284

INCOV287286

INCOV287287

INCOV287288

INCOV287289

INCOV287293

INCOV287294

INCOV287295

INCOV287296

INCOV287297

INCOV287298

INCOV287299

INCOV287300

INCOV287302

INCOV287308

INCOV287309

INCOV287310

INCOV287311

INCOV287312

INCOV287313

INCOV287372

INCOV287373

INCOV287374

INCOV287375

INCOV287376

INCOV287377

INCOV287378

INCOV287379

INCOV287380

INCOV287381

INCOV287382

INCOV287383

INCOV287384

INCOV287385

INCOV287386

INCOV287387

INCOV287388

INCOV287389

INCOV287390

INCOV287391

INCOV287392

INCOV287393

INCOV287394

INCOV287395

INCOV287396

INCOV287397

INCOV287398

INCOV287399

INCOV287400

INCOV287401

INCOV287402

INCOV287403

INCOV287404

INCOV287554

INCOV287555

INCOV287556

INCOV287558

INCOV287559

INCOV287560

INCOV287561

INCOV287562

INCOV287567

INCOV287568

INCOV287569

INCOV287570

INCOV287571

INCOV287572

INCOV287573

INCOV287574

INCOV287575

INCOV287576

INCOV287577

INCOV287578

INCOV287579

INCOV287580

INCOV287581

INCOV287585

INCOV287587

INCOV287588

INCOV287589

INCOV287590

INCOV287591

INCOV287592

INCOV287593

INCOV287893

INCOV287894

INCOV287895

INCOV287896

INCOV287897

INCOV287898

INCOV287899

INCOV287900

INCOV287901

INCOV287902

INCOV287903

INCOV287904

INCOV287905

INCOV287906

INCOV287907

INCOV287908

INCOV287909

INCOV287910

INCOV287950

INCOV287951

INCOV287952

INCOV287953

INCOV287954

INCOV287955

INCOV287956

INCOV287957

INCOV287958

INCOV287959

INCOV287961

INCOV287962

INCOV287963

INCOV287964

INCOV287965

INCOV287967

INCOV287968

INCOV287969

INCOV287970

INCOV287971

INCOV287972

INCOV287973

INCOV287974

INCOV287975

INCOV287976

INCOV287977

INCOV287978

INCOV287979

INCOV287980

INCOV287981

INCOV287982

INCOV287983

INCOV287984

INCOV287985

INCOV287986

INCOV287987

INCOV287988

INCOV287989

INCOV287990

INCOV287991

INCOV287992

INCOV287993

INCOV287994

INCOV287995

INCOV287996

INCOV287997

INCOV287998

INCOV287999

INCOV288000

INCOV288001

INCOV288002

INCOV288003

INCOV288004

INCOV288005

INCOV288006

INCOV288007

INCOV288008

INCOV288009

INCOV288012

INCOV288013

INCOV288015

INCOV288016

INCOV288017

INCOV288018

INCOV288019

INCOV288020

INCOV288021

INCOV288022

INCOV288023

INCOV288024

INCOV288025

INCOV288026

INCOV288029

INCOV288030

INCOV288031

INCOV288033

INCOV288034

INCOV288035

INCOV288036

INCOV288037

INCOV288038

INCOV288039

INCOV288040

INCOV288041

INCOV288042

INCOV288043

INCOV288045

INCOV288046

INCOV288047

INCOV288048

INCOV288049

INCOV288050

INCOV288051

INCOV288052

INCOV288053

INCOV288054

INCOV288055

INCOV288056

INCOV288057

INCOV288058

INCOV288059

INCOV288060

INCOV288061

INCOV288062

INCOV288063

INCOV288064

INCOV288065

INCOV288066

INCOV288067

INCOV288068

INCOV288069

INCOV288070

INCOV288071

INCOV288072

INCOV288073

INCOV288074

INCOV288075

INCOV288076

INCOV288077

INCOV288078

INCOV288079

INCOV288080

INCOV288081

INCOV288083

INCOV288084

INCOV288085

INCOV288087

INCOV288088

INCOV288089

INCOV288095

INCOV288096

INCOV288098

INCOV288099

INCOV288114

INCOV288116

INCOV288117

INCOV288120

INCOV288121

INCOV288122

INCOV288123

INCOV288124

INCOV288125

INCOV288126

INCOV288127

INCOV288128

INCOV288129

INCOV288130

INCOV288131

INCOV288132

INCOV288133

INCOV288134

INCOV288135

INCOV288136

INCOV288137

INCOV288138

INCOV288139

INCOV288140

INCOV288141

INCOV288142

INCOV288143

INCOV288144

INCOV288145

INCOV288146

INCOV288147

INCOV288148

INCOV288149

INCOV288150

INCOV288151

INCOV288152

INCOV288153

INCOV288154

INCOV288155

INCOV288156

INCOV288170

INCOV288171

INCOV288172

INCOV288173

INCOV288174

INCOV288175

INCOV288176

INCOV288177

INCOV288178

INCOV288179

INCOV288180

INCOV288181

INCOV288182

INCOV288183

INCOV288184

INCOV288185

INCOV288186

INCOV288207

INCOV288208

INCOV288209

INCOV288210

INCOV288211

INCOV288212

INCOV288213

INCOV288214

INCOV288215

INCOV288216

INCOV288217

INCOV288218

INCOV288219

INCOV288220

INCOV288221

INCOV288222

INCOV288223

INCOV288224

INCOV288225

INCOV288226

INCOV288227

INCOV288228

INCOV288229

INCOV288230

INCOV288231

INCOV288232

INCOV288233

INCOV288234

INCOV288235

INCOV288236

INCOV288237

INCOV288238

INCOV288239

INCOV288240

INCOV288241

INCOV288242

INCOV288243

INCOV288244

INCOV288246

INCOV288247

INCOV288248

INCOV288249

INCOV288250

INCOV288251

INCOV288252

INCOV288253

INCOV288254

INCOV288255

INCOV288256

INCOV288257

INCOV288258

INCOV288259

INCOV288260

INCOV288261

INCOV288262

INCOV288263

INCOV288264

INCOV288265

INCOV288266

INCOV288267

INCOV288268

INCOV288269

INCOV288270

INCOV288271

INCOV288272

INCOV288273

INCOV288274

INCOV288275

INCOV288276

INCOV288277

INCOV288278

INCOV288279

INCOV288280

INCOV288281

INCOV288282

INCOV288283

INCOV288284

INCOV288285

INCOV288286

INCOV288287

INCOV288288

INCOV288289

INCOV288290

INCOV288291

INCOV288292

INCOV288293

INCOV288294

INCOV288295

INCOV288296

INCOV288297

INCOV288298

INCOV288299

INCOV288300

INCOV288301

INCOV288302

INCOV288303

INCOV288304

INCOV288305

INCOV288306

INCOV288307

INCOV288308

INCOV288309

INCOV288310

INCOV288311

INCOV288312

INCOV288313

INCOV288314

INCOV288315

INCOV288316

INCOV288317

INCOV288318

INCOV288319

INCOV288320

INCOV288321

INCOV288322

INCOV288323

INCOV288324

INCOV288325

INCOV288326

INCOV288327

INCOV288328

INCOV288329

INCOV288330

INCOV288331

INCOV288332

INCOV288333

INCOV288334

INCOV288335

INCOV288336

INCOV288337

INCOV288338

INCOV288339

INCOV288340

INCOV288341

INCOV288342

INCOV288343

INCOV288344

INCOV288345

INCOV288346

INCOV288347

INCOV288348

INCOV288349

INCOV288350

INCOV288351

INCOV288352

INCOV288353

INCOV288354

INCOV288355

INCOV288356

INCOV288357

INCOV288358

INCOV288359

INCOV288360

INCOV288361

INCOV288362

INCOV288363

INCOV288364

INCOV288365

INCOV288366

INCOV288367

INCOV288368

INCOV288369

INCOV288370

INCOV288371

INCOV288372

INCOV288373

INCOV288374

INCOV288375

INCOV288376

INCOV288377

INCOV288378

INCOV288379

INCOV288380

INCOV288381

INCOV288382

INCOV288383

INCOV288384

INCOV288385

INCOV288386

INCOV288387

INCOV288388

INCOV288389

INCOV288390

INCOV288391

INCOV288392

INCOV288393

INCOV288394

INCOV288395

INCOV288396

INCOV288397

INCOV288398

INCOV288399

INCOV288400

INCOV288401

INCOV288402

INCOV288403

INCOV288404

INCOV288405

INCOV288406

INCOV288407

INCOV288408

INCOV288409

INCOV288410

INCOV288411

INCOV288412

INCOV288413

INCOV288414

INCOV288415

INCOV288416

INCOV288417

INCOV288418

INCOV288419

INCOV288420

INCOV288421

INCOV288422

INCOV288423

INCOV288424

INCOV288425

INCOV288426

INCOV288427

INCOV288428

INCOV288429

INCOV288430

INCOV288431

INCOV288432

INCOV288433

INCOV288434

INCOV288435

INCOV288436

INCOV288437

INCOV288438

INCOV288439

INCOV288440

INCOV288441

INCOV288442

INCOV288443

INCOV288444

INCOV288445

INCOV288446

INCOV288447

INCOV288448

INCOV288449

INCOV288450

INCOV288451

INCOV288452

INCOV288453

INCOV288454

INCOV288455

INCOV288456

INCOV288457

INCOV288458

INCOV288459

INCOV288460

INCOV288461

INCOV288462

INCOV288463

INCOV288464

INCOV288465

INCOV288466

INCOV288467

INCOV288468

INCOV288469

INCOV288470

INCOV288471

INCOV288472

INCOV288473

INCOV288474

INCOV288475

INCOV288476

INCOV288477

INCOV288478

INCOV288479

INCOV288480

INCOV288481

INCOV288482

INCOV288483

INCOV288484

INCOV288485

INCOV288486

INCOV288487

INCOV288488

INCOV288489

INCOV288490

INCOV288491

INCOV288492

INCOV288493

INCOV288494

INCOV288495

INCOV288496

INCOV288497

INCOV288498

INCOV288499

INCOV288500

INCOV288501

INCOV288502

INCOV288503

INCOV288504

INCOV288505

INCOV288506

INCOV288507

INCOV288508

INCOV288509

INCOV288510

INCOV288511

INCOV288512

INCOV288513

INCOV288514

INCOV288515

INCOV288516

INCOV288517

INCOV288518

INCOV288519

INCOV288520

INCOV288521

INCOV288522

INCOV288523

INCOV288524

INCOV288525

INCOV288526

INCOV288527

INCOV288528

INCOV288529

INCOV288530

INCOV288531

INCOV288532

INCOV288533

INCOV288534

INCOV288535

INCOV288536

INCOV288537

INCOV288538

INCOV288539

INCOV288540

INCOV288541

INCOV288542

INCOV288543

INCOV288544

INCOV288545

INCOV288546

INCOV288547

INCOV288548

INCOV288549

INCOV288550

INCOV288551

INCOV288552

INCOV288553

INCOV288554

INCOV288555

INCOV288556

INCOV288557

INCOV288558

INCOV288559

INCOV288560

INCOV288561

INCOV288562

INCOV288563

INCOV288564

INCOV288567

INCOV288568

INCOV288569

INCOV288570

INCOV288571

INCOV288572

INCOV288573

INCOV288574

INCOV288575

INCOV288576

INCOV288577

INCOV288578

INCOV288579

INCOV288580

INCOV288581

INCOV288582

INCOV288583

INCOV288584

INCOV288585

INCOV288586

INCOV288587

INCOV288588

INCOV288589

INCOV288590

INCOV288591

INCOV288592

INCOV288593

INCOV288594

INCOV288595

INCOV288596

INCOV288597

INCOV288598

INCOV288599

INCOV288600

INCOV288601

INCOV288602

INCOV288603

INCOV288604

INCOV288605

INCOV288606

INCOV288607

INCOV288608

INCOV288609

INCOV288610

INCOV288611

INCOV288612

INCOV288613

INCOV288614

INCOV288615

INCOV288616

INCOV288617

INCOV288618

INCOV288619

INCOV288620

INCOV288621

INCOV288622

INCOV288623

INCOV288624

INCOV288625

INCOV288626

INCOV288627

INCOV288628

INCOV288629

INCOV288630

INCOV288631

INCOV288632

INCOV288633

INCOV288634

INCOV288635

INCOV288636

INCOV288637

INCOV288638

INCOV288639

INCOV288640

INCOV288641

INCOV288642

INCOV288643

INCOV288644

INCOV288645

INCOV288646

INCOV288647

INCOV288648

INCOV288649

INCOV288650

INCOV288651

INCOV288652

INCOV288653

INCOV288654

INCOV288655

INCOV288656

INCOV288657

INCOV288658

INCOV288659

INCOV288660

INCOV288661

INCOV288662

INCOV288663

INCOV288664

INCOV288665

INCOV288666

INCOV288667

INCOV288668

INCOV288669

INCOV288670

INCOV288671

INCOV288672

INCOV288673

INCOV288674

INCOV288675

INCOV288676

INCOV288677

INCOV288678

INCOV288679

INCOV288680

INCOV288681

INCOV288682

INCOV288683

INCOV288684

INCOV288685

INCOV288686

INCOV288687

INCOV288688

INCOV288689

INCOV288690

INCOV288691

INCOV288692

INCOV288693

INCOV288694

INCOV288695

INCOV288696

INCOV288697

INCOV288698

INCOV288699

INCOV288700

INCOV288701

INCOV288702

INCOV288703

INCOV288704

INCOV288705

INCOV288706

INCOV288707

INCOV288708

INCOV288709

INCOV288710

INCOV288711

INCOV288712

INCOV288713

INCOV288714

INCOV288715

INCOV288716

INCOV288717

INCOV288718

INCOV288719

INCOV288720

INCOV288721

INCOV288722

INCOV288723

INCOV288724

INCOV288725

INCOV288726

INCOV288727

INCOV288728

INCOV288729

INCOV288730

INCOV288731

INCOV288732

INCOV288733

INCOV288734

INCOV288735

INCOV288736

INCOV288737

INCOV288738

INCOV288739

INCOV288740

INCOV288741

INCOV288742

INCOV288743

INCOV288744

INCOV288745

INCOV288746

INCOV288747

INCOV288748

INCOV288749

INCOV288750

INCOV288751

INCOV288752

INCOV288753

INCOV288754

INCOV288755

INCOV288756

INCOV288757

INCOV288758

INCOV288759

INCOV288760

INCOV288761

INCOV288762

INCOV288763

INCOV288764

INCOV288765

INCOV288766

INCOV288767

INCOV288768

INCOV288769

INCOV288770

INCOV288771

INCOV288773

INCOV288774

INCOV288775

INCOV288776

INCOV288777

INCOV288778

INCOV288779

INCOV288780

INCOV288781

INCOV288782

INCOV288783

INCOV288784

INCOV288785

INCOV288786

INCOV288787

INCOV288788

INCOV288789

INCOV288790

INCOV288791

INCOV288792

INCOV288793

INCOV288794

INCOV288795

INCOV288796

INCOV288797

INCOV288798

INCOV288799

INCOV288800

INCOV288801

INCOV288802

INCOV288803

INCOV288804

INCOV288805

INCOV288806

INCOV288807

INCOV288808

INCOV288809

INCOV288810

INCOV288811

INCOV288812

INCOV288813

INCOV288814

INCOV288815

INCOV288816

INCOV288817

INCOV288818

INCOV288819

INCOV288820

INCOV288821

INCOV288822

INCOV288823

INCOV288824

INCOV288825

INCOV288826

INCOV288827

INCOV288828

INCOV288829

INCOV288830

INCOV288831

INCOV288832

INCOV288833

INCOV288834

INCOV288835

INCOV288836

INCOV288837

INCOV288838

INCOV288839

INCOV288840

INCOV288841

INCOV288842

INCOV288843

INCOV288844

INCOV288845

INCOV288846

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