Navigating the Latest COVID-19 Challenge: Understanding the JN.1 Coronavirus Strain

Amid the ‘tripledemic’ season, staying informed about the evolving landscape of COVID-19 is crucial. Let’s explore key insights into the JN.1 coronavirus strain.

As winter drives people indoors and respiratory viruses circulate, the JN.1 strain of SARS-CoV-2, causing COVID-19, has emerged as a highly transmissible variant. While it’s challenging to predict the virus’s evolution, health authorities project increased JN.1 cases throughout the winter, leading the World Health Organization (WHO) to label it a “variant of interest.” ¹

WHO Initial Risk Evaluation of JN.1, December 19, 2023²

• JN.1 is a descendant of BA.2.86, with the earliest sample collected on August 25, 2023².
• JN.1 has an additional mutation in the spike protein called L455S compared to the parent lineage BA.2.86.
• As of December 16, 2023, 7344 JN.1 sequences have been submitted to GISAID from 41 countries, representing 27.1% of the globally available sequences from November 27 to December 3, 2023².
• France, the United States, Singapore, Canada, the United Kingdom, and Sweden have reported the largest JN.1 sequences.
• Globally, there has been a rapid increase in the proportion of JN.1 reported, with its global prevalence at 27.1% in December.
• The rapid growth is observed across all three WHO regions: the Americas, the Western Pacific, and the European regions.
• BA.2.86.1 (JN.1’s parent lineage) replication kinetics on primary nasal epithelial cells (NEC) have been observed to be no higher than other XBB-derived variants.
• It is unclear whether the high transmissibility of JN.1 in humans is associated with enhanced fitness in primary NECs and other cell types and how much of that is linked to non-spike mutations.
• Population immunity remains heterogeneous globally due to differential vaccine coverage and the circulation of SARS-CoV-2 variants worldwide.
• The immune escape potential of JN.1 depends on the immune background of the population tested.
• JN.1 displays a higher immune evasion property than BA.2.86.1 (JN.1’s parent lineage) from XBB.1.5 and EG.5.1.
• There is limited data on the cross-neutralization of JN.1, and despite the reduction in JN.1 neutralization, protection by XBB.1.5 monovalent vaccines is likely to be effective against JN.1.
• The WHO Technical Advisory Group on SARS-CoV-2 Evolution (TAG-VE) recommends that Member States prioritize specific actions to address better uncertainties relating to antibody escape and the severity of BA.2.86 and JN.1.

WHO Latest Updates on COVID-19³

• Between November 20 and December 17, 2023³, COVID-19 cases were reported in 105 countries, while COVID-19 deaths were reported in 50 countries.
• The number of reported cases has increased, while deaths have decreased during the 28 days.
• As of December 10, 2023³, the SARS-CoV-2 PCR percent positivity detected in integrated sentinel surveillance was 7.6%, reported to FluNet.
• Between November 13 and December 10, 2023³, over 118,000 new hospitalizations and over 1,600 new ICU admissions were reported.
• On December 18, 2023³, the JN.1 sub-lineage of the BA.2.86 Omicron variant was designated a separate variant of interest (VOI) from its parent lineage, BA.2.86, due to its rapid increase in prevalence in recent weeks.
• WHO tracks five VOIs – XBB.1.5, XBB.1.16, EG.5, BA.2.86, and JN.1; and five variants under monitoring (VUMs). Globally, during the 28 days from November 20 to December 17, 2023³, 105 countries reported COVID-19 cases, and 50 countries reported COVID-19 deaths.

From the available data, the number of reported cases has increased. At the same time, deaths have decreased during the 28 days, with over 850,000 new cases and over 3000 new deaths, an increase of 52% and a decrease of 8%, respectively, compared to the previous 28 days (October 23 to November 19, 2023)³. Trends in the number of reported new cases and deaths should be interpreted cautiously due to decreased testing and sequencing, alongside reporting delays in many countries.

SARS-CoV-2 PCR percent positivity, detected in integrated sentinel surveillance as part of the Global Influenza Surveillance and Response System (GISRS) and reported to FluNet, was 7.6% as of December 10, 2023³.

During the 28 days from November 13 to December 10, 2023³, 58 and 36 countries provided data at least once on COVID-19 hospitalizations and admissions to an intensive care unit (ICU), respectively. From the available data, over 118,000 new hospitalizations and over 1600 new ICU admissions were reported during the 28 days. Amongst the countries reporting these data consistently over the current and past reporting period, there was an overall increase of 23% and 51% in new hospitalizations and new ICU admissions, respectively.

On December 18, 2023³, JN.1, a sub-lineage of the BA.2.86 Omicron variant, was designated a separate VOI, apart from its parent lineage BA.2.86, due to its rapid increase in prevalence in recent weeks. JN.1 accounted for 27.1% of sequences in December compared to 3.3% in November. WHO currently tracks several SARS-CoV-2 variants: five VOIs – XBB.1.5, XBB.1.16, EG.5 and BA.2.86 and JN.1; and five VUMs. Globally, EG.5 remains to be the most reported VOI. However, it has shown a declining trend over the past few weeks, accounting for 36.3% of sequences shared on GISAID in December compared to 53.7% in November.

Global Impact of JN.1¹

The JN.1 variant has reached several countries, affecting daily life and healthcare systems.

1) Singapore
With JN.1 accounting for around 60% of infections, Singapore has significantly increased COVID cases as per the information from government sources. The government has responded with additional treatment facilities, mask mandates in crowded places, and encouragement for vaccinations.

2) Indonesia
Experiencing a 13% rise in COVID cases, Indonesia emphasizes booster doses and preventive measures to control infections. Based on information from government sources, Jakarta, the capital, registers an average of 200 instances daily, mostly asymptomatic or mildly symptomatic.

3) Malaysia
Facing a nearly doubled infection rate in a week, Malaysia focuses on community tracing and advises mask-wearing. The government rules out lockdown but urges precautions, especially for senior citizens and those with underlying health conditions.

4) China
China reports a low epidemic level of JN.1 cases, with mild and asymptomatic infections. While the numbers are limited, health authorities remain vigilant about the variant’s potential impact.

5) The Philippines
Experiencing an uptick in COVID and flu-like illnesses, the Philippines records mild symptoms in most cases as per the information from government sources. President Ferdinand Marcos Jr. tested positive for COVID, highlighting the widespread impact.

Conclusion^1,2,3

In conclusion, the emergence of the JN.1 coronavirus strain underscores the ongoing challenges posed by the ever-evolving nature of SARS-CoV-2. While specifics about this variant are still unfolding, individuals must stay informed and adhere to recommended preventive measures. The ‘tripledemic’ season, coinciding with SARS-CoV-2, influenza, and RSV, emphasizes the importance of updated vaccinations and vigilant protective efforts.

As the global impact of JN.1 is felt in countries like Singapore, Indonesia, Malaysia, China, and the Philippines, each region is adapting with additional healthcare measures and encouraging vaccination campaigns. The situation highlights the interconnectedness of the world in facing health challenges.

Collaboration, timely information sharing, and adherence to public health guidelines will be pivotal in mitigating the impact of emerging variants. Individuals are urged to prioritize their health, follow local policies, and contribute collectively to the ongoing efforts to navigate the complexities of the ‘tripledemic’ and the challenges posed by new coronavirus sub-variants like JN.1. As we navigate this complex landscape, it is essential to stay united, informed, and resilient in the face of evolving health threats.

---

References

1. Bureau AN. Covid: 50,000 Cases In Singapore, JN.1 Variant Detected In Indonesia, Malaysia Too [Internet]. news.abplive.com. 2023 [cited 2024 Jan 2]. Available from: https://news.abplive.com/health/covid-variant-jn1-cases-rising-asian-countries-singapore-china-indonesia-malaysia-india-1650846
2. WHO. SARS-CoV-2 Initial Risk Evaluation of JN.1. Available from: https://www.who.int/docs/default-source/coronaviruse/18122023_jn.1_ire_clean.pdf?sfvrsn=6103754a_3
3. COVID-19 epidemiological update – 22 December 2023 [Internet]. www.who.int. Available from: https://www.who.int/publications/m/item/covid-19-epidemiological-update—22-december-2023