Evolution of SARS-CoV-2 from BA.2.86 to JN.1 variations and detection in Bangladesh

To the Editor

The SARS-CoV-2 virus caused the COVID-19 pandemic and subsequent worldwide health issues because of the introduction of many subvariants, including Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa, Lambda, Mu, and Omicron (Sheeza et al. 2024). Every variation has its own unique set of challenges. Moreover, the COVID-19 infection induces several cytokines, including TNF, IL-1β, and IL-6, as well as pro-inflammatory chemokines including CCL20, CXCL1, CXCL2, CXCL3, CXCL5, CXCL6, and CXCL16 (Marlia et al. 2024). On the other hand, the SARS-CoV-2 saltation variation BA.2.86 has drawn attention across the world and was immediately identified as a variety under surveillance upon its appearance. BA.2.86 was first discovered in August 2023, is phylogenetically distinct from the circulating SARS-CoV-2 omicron XBB lineages, which include EG.5.1 and HK.3 (Satapathy et al. 2024). The spike protein of BA.2.86 has more than thirty mutations, it has a higher potential for immune evasion than XBB and BA.2. Furthermore, BA.2.86 showed a very high affinity for ACE2 binding but lacked a considerable growth advantage and humoral immune escape, when compared to current dominant variants like EG.5.1 and HK.3 (Yang et al. 2024). The development of BA.2.86 led to the appearance of JN.1 (BA.2.86.1.1) (Pirola) in late 2023 (Kaku et al. 2024; Satapathy et al. 2024). Therefore, natural immunity could be involved in warding off the illness. Herd immunity may be important if JN.1 spreads rapidly because some individuals have not yet gotten their vaccinations. Public awareness of social distance and other personal hygiene measures should also be reemphasized (Marlia et al. 2024).

A Variant of Interest (VOI) is a term used by the World Health Organization (WHO) to describe a SARS-CoV-2 variant with genetic changes that are known to affect how the virus behaves or its potential impact on human health (WHO 2023). JN.1 has been officially recognized as an autonomous VOI by the World Health Organization (WHO) (Looi 2023) and it is varied from BA2.86 by a mutation in spike protein (Leu455Phe) Which enhances transmissibility and immunological escape capability, is present in JN.1, HK.3, and other flip variations (Kaku et al. 2024). Furthermore, it features 26nt deletion in the 3′-UTR, 31ERS deletion in the N-protein, and 24LPP, 69HV, 145Y, 211N (208N in BA.2), and 483 V (480 V in BA.2) deletions in the spike. A study has identified other JN.1 spike mutations that may also be relevant, including 442N = H249N, 261D = A268D, 352 T = K360T, 400 K = R407K, 442H = P449H, 449W = L456W, 474 K = N485K, 480 K = A488K, and 566 V = A574V (CHAKRABORTY, 2024). Due to a mutation in a single spike protein, this variety could be able to evade immune system recognition. The capacity of neutralizing antibodies to recognize and neutralize the spike protein is hampered by its transformation into a whole new hazard (Roney et al. 2024). Since its initial discovery in September 2023 in the USA, it has quickly spread throughout the country and already makes up a sizable fraction of the circulating variations (CDC 2024).

According to Forbes 2023 report, six mutations (T24I, V238L, G489S, K1155R, V1227I, and T1228I) have been found in the NSP3 protein of JN.1. NSP3 is a large non-structural protein which is essential for both immune evasion and viral proliferation. The function of the protein may be affected by these alterations, which may also improve the capacity to elude the host immune system or replicate more quickly of the virus. In addition to the spike protein, JN.1 also carries mutations in the nucleocapsid (N) protein, and the N-protein is required for the packaging and assembly of viral genomes. Modifications to this protein might affect the pathogenicity and capacity for replication of the virus. Beyond just the changes in the spike protein (Leu455Phe), mutations in non-spike proteins of JN.1, such NSP3 and N, may also be responsible for the increased transmissibility and immune evasion abilities of variant. These alterations may have an impact on the pathogenesis, replication, and capacity of the virus to elude host immune responses. To completely comprehend the effect of these non-spike protein mutations on the general traits of the JN.1 variation, more investigation is required (Forbes 2023).

JN.1 is phylogenetically different from the other SARS-CoV-2 mutations, and it has been identified as the most immune-evading variant. It has a substantially higher dissociation constant (KD) for the receptor-binding domain (RBD) compared to other variants, indicating weaker binding to the ACE2 receptor (Satapathy et al. 2024). Furthermore, L455S mutation likely contributes to the higher KD value and reduced ACE2 binding affinity observed for JN.1. Despite the weaker RBD-ACE2 interaction, the JN.1 variant has demonstrated significantly higher infectivity in pseudovirus experiments. This suggests that the enhanced infectivity of JN.1 is not solely dependent on ACE2 binding and may involve other factors, such as immune evasion or altered viral entry mechanisms (Yang et al. 2024). It is now the type with the fastest rate of development in countries including the US, France, Singapore, Canada, the UK, and Sweden, with documentation from more than 41 countries (Hemo and Islam 2024). Notably, JN.1 is primarily responsible for the increase in COVID-19 cases in Singapore, and its emergence in India has given rise to grave worries (Satapathy et al. 2024). Figure 1 provides an explanation of the genetic basis for how viruses undergo alterations in their genomes throughout time. These changes can have a substantial effect on the traits of the viruses as well as how they interact with humans and other host animals. Comprehending these systems is essential to formulating efficacious tactics against viral infections.

Fig. 1

Viral mutation mechanisms and the appearance of novel variations (Satapathy et al. 2024)

The COVID-19 pandemic had a devastating effect on Bangladesh and the first confirmed case was identified on March 8, 2020 (Islam et al. 2020). Moreover, the cases of all districts were reported by early of May, and the cumulative number of cases in Bangladesh surpassed that of China on June 13, (Rahman et al. 2021). Bangladesh had around 2,049,377 cases and 29,493 fatalities as of April 13, 2024 (Worldometers 2024). The government of Bangladesh launched a national COVID-19 vaccination campaign on February 7, 2021, using 7 million doses of the vaccine made by Oxford and AstraZeneca. Several more vaccines, including those made by Johnson & Johnson, Sinovac, Sinopharm, Pfizer-BioNTech, and Sputnik V, have now been approved for use by the government. As of February 26, 2024, 83.07% of the population in Bangladesh had received all recommended doses of the COVID-19 vaccination, and over 90% of the population had received at least one dose (Nazmunnahar et al. 2023).

The Institute of Epidemiology, Disease Control and Research (IEDCR) reported that JN.1 was found in samples from five individuals in Bangladesh, both from Dhaka and other locations, who had no history of recent travel (AA.com 2024; TheDailySTar 2024; TBNews 2024; DhakaTribune 2024; DBNews 2024). The health officials in Bangladesh advise the public not to panic because current vaccines will protect against life-threatening and severe illness caused by JN.1 and other COVID-19 variants that are circulating (TBNews 2024; DBNews 2024). The rise in morbidity prompted the Directorate General of Health Services (DGHS) to issue a notification directing the authorities to resume the first, second and booster doses of the COVID-19 vaccine program (TBNews 2024).

Nasopharyngeal swab specimens were requested from individuals across the country displaying COVID-19 symptoms as part of the regular SARS-CoV-2 diagnostic screening for the Respiratory Virus Genomic Surveillance in Bangladesh (Table 1). Real-time reverse transcription polymerase chain reaction (rRT-PCR) was utilized to target the new coronavirus (2019-nCoV) following the isolation of viral RNA using the QIAamp viral RNA micro kit (Qiagen, Germany). This was done using a nucleic acid test kit from Sansure Biotech in China. Eighteen and fourteen positive samples from routine surveillance with a cycle threshold (C_T) value of less than 27 for whole genome sequencing, in accordance with the amplicon-based SARS-CoV-2 sequencing protocol created by ARTIC Network (Tahsin et al. 2024). ARTIC v4.1 primer panels were used in the sequencing library preparation process. This method included multiplex PCR using Q5 high-fidelity DNA polymerase (New England Biolabs, USA) and the synthesis of viral cDNA using the LunaScript RT SuperMix Kit (New England Biolabs, USA). NEBNext Ultra II end repair/dA-tailing module (New England Biolabs, USA) was used to handle amplicons. Amplicons were combined into a single reaction tube after native barcode (EXP-NBD104 and EXP-NBD114) ligation (Oxford Nanopore Technologies, UK) using blunt/TA DNA ligase (New England Biolabs, USA). The completed DNA library was loaded into a FLO-MIN106D flow cell (R9.4.1) after adaptor ligation with NEBNext Quick T4 DNA ligase (New England Biolabs, USA). For a minimum of six hours, sequencing was done using a MinION Mk1C sequencing apparatus using the factory quality score filter (Q-score = 8). Using the Fast base-calling model on MinKNOW v22.12.5 (bionic), demultiplexing and base calling of raw readings were done. The readings that were processed were assembled using the ARTIC guppyplex code script. On ARTIC EPI2ME desktop agent v3.7.3, consensus sequences in fasta format were created using Medaka v1.4 (https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html). Moreover, the phylogenetic tree was depicted in Fig. 2 for forty-three (43) viral genomes including research strains.

Table 1 Information about the Omicron JN.1 sub-lineage of Bangladesh SARS-CoV-2

Fig. 2

Molecular evolution of coding-complete Genomes of the Omicron sub-lineage JN.1 of SARS-CoV-2. Forty-three (43) viral genomes in all, including research strains, are shown. Augur was used to construct and annotate the tree. The color of a tip is determined by ancestry. Divergence indicates the length of the branch (Jony et al. 2024)

JN.1 developed an extra mutation in spike protein (L455S) and six mutations (T24I, V238L, G489S, K1155R, V1227I, and T1228I) in NP3 non-spike protein to its parent BA.2.86 variant as compared to the reference Wuhan Hu-1 SARS-CoV-2 genome (GenBank accession NC_045512.2). As a result, JN.1 is presently responsible for the greatest incidence of SARS-CoV-2 infection globally (Kaku et al. 2024; Khan et al. 2024; Marlia et al. 2024). Furthermore, BA.2.86 shows significant evolutionary drift and more than 30 spike-glycoprotein changes compared to its parent Omicron BA.2, suggesting a great potential for immune evasion (Tahsin et al. 2024). The descending JN.1.4 and JN.1.11, which are derived from JN.1, have distinct differences in the amino acids of their ORF1a-protein (T1701I) and spike protein (V1104L), respectively. The rapid spread of these mutations across Bangladesh may suggest that they were carried there by unaffiliated parties. Therefore, continuous genomic monitoring is required to monitor newly emerging SARS-CoV-2 strains in order to facilitate effective public health planning and implementation.

The spike protein of JN.1 carries about 30 mutations, including a new mutation (L455S), which makes it harder for antibodies to attach to the virus and stop infection (Khan et al. 2024; Marlia et al. 2024). This could lead to increased immune evasion compared to previous variants (Khan et al. 2024). Bangladesh faces several challenges that could exacerbate the spread of JN.1. The country has a high population density and an inadequate water surveillance system, raising the possibility of rapid transmission. The medical infrastructure and shortage of healthcare professionals of Bangladesh may also struggle to handle a severe outbreak (Marlia et al. 2024). Additionally, public awareness about COVID-19 prevention measures has decreased since the WHO ended the public health emergency declaration in May 2023. Around 10 million individuals in Bangladesh are still without their second vaccine dose, leaving them vulnerable. The vaccines used previously may also provide limited protection against the mutated JN.1 strain. To mitigate the risks, Bangladesh should focus on improving hospital facilities, conducting investigations on the continued validity of previous pandemic response measures, and promoting adjuvant antiviral and vaccination therapies. Raising public awareness about personal hygiene and social distancing will also be crucial to combat the potential spread of the JN.1 variant (Marlia et al. 2024). The following are the key recommendations for Bangladeshi public health authorities about the COVID-19 JN.1 variant:

Enhance surveillance and testing

• 1. Increase COVID-19 testing capacity, especially in high-risk areas, to rapidly identify any JN.1 cases.

• 2. Conduct genomic sequencing on a representative sample of positive cases to track the spread and evolution of the JN.1 variant.

• 3. Strengthen disease surveillance systems to quickly detect any significant increases in COVID-19 transmission.

Strengthen healthcare preparedness

• 1. Ensure hospitals and healthcare facilities have sufficient medical supplies, equipment, and staffing to handle a potential surge in COVID-19 patients.

• 2. Implement contingency plans to rapidly scale up healthcare capacity if needed, such as setting up additional treatment centers.

• 3. Prioritize vaccination efforts, especially for high-risk populations, to reduce severe illness and hospitalizations.

Enhance public health messaging

• 1. Communicate clearly with the public about the JN.1 variant, its potential risks, and the importance of continued preventive measures.

• 2. Encourage adherence to COVID-19 safety protocols such as masking, distancing, and testing among the general population.

Furthermore, the government of Bangladesh has implemented many strategies to curb the proliferation of the JN.1 COVID-19 variant:

• 1. In response to an upsurge in diseases, the Directorate General of Health Services (DGHS) has sent a notification asking authorities to begin the COVID-19 vaccination programme for first, second, and booster doses (TBNews 2024; AA.com 2024).

• 2. Health officials have advised the public not to worry since JN.1 and other circulating COVID-19 variations will not cause serious illness or death if current vaccinations are administered (TBNews 2024; TheDailyStar 2024).

• 3. Five people from Dhaka and other areas who had no history of recent travel were tested for JN.1, and the Institute of Epidemiology, Disease Control and Research (IEDCR) verified this finding (Marlia et al. 2024; TBNews 2024; TheDailyStar 2024).

• 4. Despite being less severe, JN.1 has been designated as a variation of interest by WHO because of its potential for rapid dissemination (DhakaTribune 2024; TBNews 2024).

• 5. Nearly 30,000 people have perished and over 2 million out of 170 million people have contracted COVID-19 since the virus's first cases were verified in Bangladesh in March 2020 (DhakaTribune 2024; AA.com 2024).

In Bangladesh, where COVID-19 was first identified in March 2020, about 2 million of the country's 170 million inhabitants have fallen ill. Approximately 30,000 people have died from the virus. Overall, the detection of JN.1 in Bangladesh highlights the need for continued vigilance and public awareness to combat the spread of the virus and ensure the effectiveness of vaccination efforts.