What We Know about JN.1 (BA.2.86.1.1) SARS-CoV-2 Variant

Abstract

Background: JN.1 (BA.2.86.1.1) has become the dominant strain in the U.S. at the end of 2023 according to the U.S. Centers for Disease Control and Prevention. The strain is a descendant of EG.5 family that was identified in China in February 2023 and was first detected in the United States in April 2023. JN.1* SARSCoV2 lineages: JN.1 (BA.2.86.1.1), JN.1.1, JN.1.1.1, JN.1.2, JN.1.3 and recombinants XDD (EG.5.1.1/JN.1), XDK (XBB*/JN.1.1.1). There is only a single change between JN.1 and BA.2.86 in the spike protein. JN.1 has inherited more than 30 mutations in its spike protein. It also acquired a new mutation,L455S, which further decreases the ability of antibodies to bind to the virus and prevent infection. A nonspike protein that is heavily mutated in JN.1 is the NSP3 protein. There are six mutations in NSP3 protein, namely T24I, V238L, G489S, K1155R, N1708S, and A1892T. NSP3 is one of the most active proteins in the virus, playing roles in viral RNA binding, polyprotein processing, and other functions. While the exact function of these mutations is unknown, they are likely to increase the efficiency of many of these mechanisms, creating a more functional and pathogenetic virus.The N protein is heavily mutated, R203K and G204R have been mutated in most virus variants throughout the pandemic and likely improve viral replication rate. The other mutations in N may also work to improve viral replication. While the Orf8 protein is truncated in the widespread XBB.1.5 variant, it is fully present in JN.1.

The symptoms of JN.1 appear to be similar to those caused by other strains, which include sore throat, congestion, runny nose, cough, fatigue, headache, muscle aches, fever or chills, loss of sense of taste or smell, shortness of breath or difficulty breathing, nausea or vomiting and diarrhea.

Some doctors have reported that upper respiratory symptoms seem to follow a pattern of starting with a sore throat, followed by congestion and a cough.

Aim: The purpose of the manuscript is to present a systematic review on the prevalence, structural, genomic, and pathogenic characteristics of JN.1 from January 1 to February 29, 2024, emphasizing on the variant genetic characteristics, contagiousness, and potential pathogenicity.

Material and Methods: Original scientific articles published in Medline, Pubmed, Science Direct, Web of Science, Scopus, EBSCO and BioMed Central databases, official health organizations (World Health Organization, U.S. Centers for Disease Control and Prevention, European Centre for Disease Prevention and Control) electronic publications, and specialized media in the subject, were electronically searched to accomplish the aim of the study. Articles published in any language were included from January 2024 to present using a variety of keywords in combination. The studies relevant to our review were analysed and compared.

Results and Discussion: The step-change evolution of BA.2.86, combined with the immune-evading features in JN.1, has given the virus a global growth advantage well beyond the XBB.1-based lineages the world faced in 2023. Evidence suggests the human adaptive immune system could still recognise and respond to BA.286 and JN.1 effectively. Updated monovalent vaccines, tests and treatments remain effective against JN.1. There are two elements to “severity”: first if it is more ‘intrinsically’ severe (worse illness with an infection in the absence of any immunity) and second if the virus has greater transmission, causing greater illness and deaths, simply because it infects more people. The latter is certainly the case with JN.1.

Conclusions: The latest data from US-CDC shows JN.1 as the prevalent SARS-CoV-2 variant in the United States. JN.1 in January 2024, quickly increase its prevalence and surpassed other variants, including HV.1 to become the most prevalent strain in The United States of América. JN.1 has a similar transmission rate, exhibits a greater evasive capacity of immune-generated antibodies than HV.1 family of SARS-CoV-2, produce similar symptoms that of other Omicron variants, are expected not to produce an increase in hospitalizations and mortality rate and the SARS-CoV-2 vaccines recently developed by Pfizer and Moderna, must be effective against this Omicron subvariant. For now, the dominant variant JN.1 does not seem harmful in terms of creating a deadly disease but is still contagious enough to not be ignored.