COVID-19 variant JN.1 + KP.2, PJ.2

[sharon sanders]

Executive Summary

Previously, JN.1 was tracked as part of BA.2.86, the parent lineage that is classified as a variant of interest (VOI). However, in recent weeks, JN.1 continues to be reported in multiple countries, and its prevalence has been rapidly increasing globally and now represents the vast majority of BA.2.86 descendent lineages reported to GISAID. Due to its rapidly increasing spread, WHO is classifying JN.1 as a separate variant of interest (VOI) from the parent lineage BA.2.86. Considering the available, yet limited evidence, the additional public health risk posed by JN.1 is currently evaluated as low at the global level. It is anticipated that this variant may cause an increase in SARS-CoV-2 cases amid surge of infections of other viral and bacterial infections, especially in countries entering the winter season. Following discussions with the WHO Technical Advisory Group for Virus Evolution (TAG-VE) and considering the data at hand, current population immunity globally as well as immunity generated by XBB.1.5 booster vaccination is expected to remain cross-reactive to this variant, against symptomatic and severe disease. Therefore, the spread of this variant will unlikely increase the burden on national public health systems compared to other Omicron sublineages. However, countries approaching the winter season should be aware that, altogether, SARS-CoV-2 and co-circulating pathogens may exacerbate the respiratory disease burden.

more... https://www.who.int/docs/default-source/coronaviruse/18122023_jn.1_ire_clean.pdf?sfvrsn=6103754a_3

 

[Lance]

CIDRAP- Respiratory virus levels climb as JN.1 dominates COVID detections

https://www.cidrap.umn.edu/covid-19/respiratory-virus-levels-climb-jn1-dominates-covid-detections

Respiratory virus levels climb as JN.1 dominates COVID detections


Lisa Schnirring


39 minutes ago.

COVID-19

Influenza, General

Respiratory Syncytial Virus (RSV)

​

Respiratory illness activity is elevated or increasing across most of the United States, and JN.1 is now the dominant SARS-CoV-2 variant, the Centers for Disease Control and Prevention (CDC) said in its latest updates just before Christmas.

In its tracking of three main viruses that drive visits to health providers for symptoms such as fever and sore throat, the CDC said respiratory syncytial virus (RSV) activity remains elevated, especially for young children. Meanwhile, COVID-19 activity is increasing in many parts of the country, as is seasonal flu, though hospital bed occupancy and intensive care unit (ICU) capacity for all patients remains stable.

ED visits for COVID highest in infants and seniors


The CDC's two main severity markers rose compared to the previous week, with hospitalizations up 10.4% and deaths up 3.4%. States in the Midwest and Northeast have numerous counties at the medium level for COVID hospital admissions, with some counties in those regions listed at the high level.

Nationally, only 3% of deaths were due to COVID during the reporting period, with higher levels reported by a few states: Kentucky, Missouri, Iowa, Minnesota, Maryland, and Massachusetts. The CDC characterized the COVID death trend as stable.

The CDC's early indicators also reflected rises, with emergency department (ED) visits up 6.6% compared to the previous week and test positivity showing a slight rise. The marker rose to the substantial level in Iowa, and Illinois, Michigan, and Indiana were at the moderate level.

ED visits for COVID were highest in infants and older adults but were also elevated in young children, the CDC said in its latest respiratory virus snapshot.

Nationally, test positivity was 11.7% and was highest in the lower Midwest, followed by the rest of the Midwest, the Northeast, and the Southwest.

JN.1 vaults to top lineage


The proportion of JN.1 viruses over the past 2 weeks was up sharply, rising from 21.3% to 44.2%, the CDC said in its latest estimates, putting it far above the next most common variant, HV.1. In a separate update on JN.1, the CDC said it is also seeing an increasing share of infections caused by JN.1 in travelers, wastewater, and most world regions.

"JN.1's continued growth suggests that the variant is either more transmissible or better at evading our immune systems than other circulating variants. It is too early to know whether or to what extent JN.1 will cause an increase in infections or hospitalizations," the CDC said, adding that existing vaccines, tests, and treatments still work against JN.1.

JN.1, under the BA.2.86 umbrella, has the L455S mutation in the spike protein, which is thought to increase its immune-evasion capabilities. Last week, the World Health Organization (WHO) designated JN.1 as its own variant of interest, following a rapid increase in proportions at the global level.

Both the WHO and CDC have said JN.1 doesn't seem to pose a bigger public health risk than other variants, though it could trigger fresh COVID surges at a time when other respiratory viruses are circulating.

Flu markers climb higher


Meanwhile, flu activity continues to rise in all regions of the United States, the CDC said in its latest update. The highest levels have been in the southern tier of states, with Louisiana and South Carolina now listed at the top of the CDC's "very high" category, which stands out as blue among varying shades of red in the high and very high categories.

The 2009 H1N1 virus is still the predominant strain, but the CDC said it has also received reports of H3N2 and influenza B viruses.

ED visits for flu are on the rise, especially in school-age children, and test positivity for the virus also continues to increase, at 12.8% at clinical labs. Hospitalizations for flu continue an upward trend, affecting all age-groups, with the highest rates in seniors.

No new pediatric flu deaths were reported last week, keeping the season's total at 14.

Global COVID picture


In its monthly profile of COVID activity, the WHO said cases have risen 52% over the last 28 days, while deaths declined by 8%. However, the WHO emphasized that few countries are testing and reporting cases and that trends aren't likely to accurately reflect the global picture.

At the regional level, four areas reported rises in new COVID cases, most dramatically in South East Asia, followed by Africa, the Western Pacific, and Europe. Deaths were up in South East Asia, as well as—to a lesser degree—Europe.

Of the few countries that regularly report hospital data, the data suggest hospitalizations were up 23% and a 51% rise in new ICU admissions for COVID.
​

 

[Pathfinder]

UPDATED: Egypt detects first two cases of new COVID-19 variant JN.1

Ahram Online , Thursday 28 Dec 2023

Egypt's Ministry of Health and Population announced in a statement on Thursday the detection of the first two cases of the new Omicron coronavirus subvariant JN.1, following laboratory tests.

The identified cases were in stable health conditions, with mild symptoms only affecting the upper respiratory tract, the ministry statement explained, noting that they did not need to be hospitalized.

The ministry reassured that there was no update related to the precautionary measures recommended by the World Health Organization (WHO) to approach respiratory system infections, including coronavirus, influenza, and other rhinoviruses.

The statement recommended continuous cleaning and disinfection of hands and surfaces, urging the infected to wear face masks in public places.

Egypt is currently witnessing an increase in respiratory infections, ranging between minor and moderate cases, which are normal at this point of the year, Mohamed Awad Tag El-Din, presidential adviser for health affairs, said on Sunday.
...

https://english.ahram.org.eg/NewsCo...ypt-detects-first-two-cases-of-new-COVID.aspx

 

[Mary Wilson]

Multiple JN.1* branches with S:F456L #1253 - GitHub

aviczhl2 commented Jan 4, 2024​

It seems that S:F456L is very convergent in JN.1 now.

General query: T3565C,C18894T,T22926C, Spike_F456L (27 seqs)

• Branch 1: JN.1.1+S:G181E+S:F456L, Issue JN.1.1 plus S:G181E (35) with a sub-lineage with S:F456L (7) France, Switzerland, Belgium #1147
• Branch 2: JN.1.1+S:F456L, Issue Another JN.1.1+S:F456L(3 seqs, 2 countries) #1249
• Branch 3: JN.1+S:F456L, Query: T22928C, T3565C, T22926C, -C1762A, -18453, -18093, -2782, -3589,-7113, 10 seqs, UK, Canada
• Branch 4: JN.1 with S:V1104L parental of SLip Branch 4 of #1253 emerged in India ( 10-11 seqs) #1262+Orf1a:T2283I,S:F456L Query: C7113T,T22928C,T3565C, 3 seqs, India

Doublets:

Singlets

1. JN.1 sublineage with ORF1a:T170I, ORF1b:G662S, and T18453C first detected in Denmark (73 GISAID seqs as of 2024-01-05; Denmark, Belgium, Finland, Sweden, USA) #1155+Orf1a:T4087I+S:F456L Query: T18453C, C12525T,T22928C, USA
2. JN.1+T18453C with C28201T（ORF8:S103L）（1272seqs） #1171+S:F456L Query: C28201T, T22928C, T22926C, Sweden
3. JN.1.1+Orf1a:E4388K+S:F456L Query: G13427A, T22928C, C9142T, Brazil
4. JN.1+A18093G+S:F456L Query: A18093G, T22928C,T3565C, Singapore
5. JN.1+G2782T+S:F456L Query: G2782T, T22928C, T3565C, USA
6. JN.1+C3589T+S:F456L Query: C3589T,T22928C,T3565C,France

​ ...

https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
​

 

[Pathfinder]

Translation Google

TUNISIA Exclusive-Tunisia: 1st case of contamination by the new variant of coronavirus JN.1 (Video)

By Nadia.Ben.Tamansourt | 5 hours ago


Riadh Daghfous, director general of the National Pharmacovigilance Center (CNPV) and member of the scientific committee to fight the coronavirus, announced, this Wednesday, January 24, 2024 to Tunisie Numérique, the recording of a first case of contamination by the new variant of Coronavirus JN.1

Daghfous explained that the latest genomic sequencing showed the appearance of this new variant in Tunisia.

It is recalled that the World Health Organization (WHO) has issued a new warning in recent hours regarding the new variant of COVID-19 JN.1, which has begun to spread rapidly in a number of countries around the world, this which sparked fear and dread of reliving the difficult experience of COVID-19.

The WHO has classified the new JN.1 variant as “interesting” and distinct from the parent BA.2.86 strain, after previously classifying it as a sub-variant of that strain.

She urged citizens to take necessary steps to protect themselves from infection and serious illness by using all available tools, chief among them masks, after the virus was classified as highly contagious and spreading rapidly.

https://www.tunisienumerique.com/ex...le-nouveau-variant-du-coronavirus-jn-1-video/

 

[sharon sanders]

Virological characteristics of the SARS-CoV-2 KP.2 variant

Yu Kaku, Keiya Uriu, Yusuke Kosugi, Kaho Okumura, Daichi Yamasoba, Yoshifumi Uwamino, Jin Kuramochi, Kenji Sadamasu, Kazuhisa Yoshimura, Hiroyuki Asakura, Mami Nagashima, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Jumpei Ito, Kei Sato
doi: https://doi.org/10.1101/2024.04.24.590786
This article is a preprint and has not been certified by peer review [what does this mean?].
00011001765

Abstract


The JN.1 variant (BA.2.86.1.1), arising from BA.2.86(.1) with the S:L455S substitution, exhibited increased fitness and outcompeted the previous dominant XBB lineage by the biggening of 2024. JN.1 subsequently diversified, leading to the emergence of descendants with spike (S) protein substitutions such as S:R346T and S:F456L. Particularly, the KP.2 (JN.1.11.1.2) variant, a descendant of JN.1 bearing both S:R346T and S:F456L, is rapidly spreading in multiple regions as of April 2024. Here, we investigated the virological properties of KP.2. KP.2 has three substitutions in the S protein including the two above and additional one substitution in non-S protein compared with JN.1. We estimated the relative effective reproduction number (R[SUB]e[/SUB]) of KP.2 based on the genome surveillance data from the USA, United Kingdom, and Canada where >30 sequences of KP.2 has been reported, using a Bayesian multinomial logistic model. The R[SUB]e[/SUB] of KP.2 is 1.22-, 1.32-, and 1.26-times higher than that of JN.1 in USA, United Kingdom, and Canada, respectively. These results suggest that KP.2 has higher viral fitness and potentially becomes the predominant lineage worldwide. Indeed, as of the beginning of April 2024, the estimated variant frequency of KP.2 has already reached 20% in United Kingdom.

The pseudovirus assay showed that the infectivity of KP.2 is significantly (10.5-fold) lower than that of JN.1. We then performed a neutralization assay using monovalent XBB.1.5 vaccine sera and breakthrough infection (BTI) sera with XBB.1.5, EG.5, HK.3 and JN.1 infections. In all cases, the 50% neutralization titer (NT[SUB]50[/SUB]) against KP.2 was significantly lower than that against JN.1. Particularly, KP.2 shows the most significant resistance to the sera of monovalent XBB.1.5 vaccinee without infection (3.1-fold) as well as those who with infection (1.8-fold). Altogether, these results suggest that the increased immune resistance ability of KP.2 partially contributes to the higher R[SUB]e[/SUB] more than previous variants including JN.1.
​
more... https://www.biorxiv.org/content/10.1101/2024.04.24.590786v1

 

[sharon sanders]

By Katia Hetter, CNN
4 minute read
Published 8:30 AM EDT, Thu May 23, 2024​

There is a new coronavirus variant in town. KP.2, a member of the so-called FliRT variants, nicknamed after their mutations, has become the dominant coronavirus strain in the United States, according to the US Centers for Disease Control and Prevention. These FliRT variants have certain mutations in common but are still part of the Omicron family of the coronavirus.

For the period from April 28 to May 11, nearly 30% of new cases were caused by KP.2, up from less than 16% in the two-week period before that.
​
more... https://www.cnn.com/2024/05/23/health/kp2-covid-flirt-variant-wellness/index.html

 

[sharon sanders]

my bolding


Raj Rajnarayanan
@RajlabN


Tracking #SARSCoV2 #Lineages - Globally |07/27/24 Top lineages -#30DayTrends
KP.3.1.1 (17.4%)
KP.2.3 (8.1%)
KP.3.3 (8%)
KP.3.1 (7.2%)
KP.3 (3.3%)
KP.2 (3.1%)
KP.3.1.4 (3.1%)
KP.3.2 (3%)
LB.1 (2.5%)
KP.3.2.3 (2.5%)

Track #G30 : https://public.tableau.com/app/profile/raj.rajnarayanan/viz/ConvergentLineages-VariantSoup-World/G20…​

 

[sharon sanders]

updated....