15 new sequences from Spain 🇪🇸, collected in June and July 2026: 2 × XFJ* 6 × XFG* 7 × BA.3.2* #BA32 continues to be highly prevalent in Spain.

NYT: Cyclospora Linked to Taylor Farms Lettuce Sent to Taco Bell By Christina Jewett, Alice Callahan and Caroline Hopkins Legaspi nyti.ms/4hhYAPx

WSJ: In Congo, Ebola Responders Fear WhatsApp Voice Notes Are Spreading Fake News by Nicholas Bariyo on.wsj.com/4w9h5uj

Large multistate cyclosporiasis outbreak in the US linked to imported iceberg lettuce Read more at: https://beaconbio.org/en/report/?reportid=fc3849c7-5f64-46b0-931a-c84ccb5e21d3&eventid=f4c53ac1-a8bb-4baf-b97b-4b764df4f66d&utm_source=bluesky&utm_medium=social&utm_campaign=socialpost

#CDC reported today that it has been informed of 2 more pediatric #flu deaths in the 2025-26 season. The deaths occurred in March. That brings the total for this season to 187 peds flu deaths, though the number could continue to climb as late reports come in. www.cdc.gov/fluview/surv...

Costa Rica reports third confirmed case of mpox in 2026 with documented local transmission chain Read more at: https://beaconbio.org/en/report/?reportid=78f1a449-b988-4271-89eb-e03afc644b52&eventid=6fa82aaf-56bc-4b5f-aa29-36be9edf8cc1&utm_source=bluesky&utm_medium=social&utm_campaign=socialpost

July 17th Update: A notable uptick is visible on WWScan, with numbers doubling in the past month. We are still only about half or our previous lull levels, but we should continue to see increases. This wave should be limited in potential. 🔸~88,000 new inf/day 🔸~1 in 750 currently infectious

A route of BA.3.2 transmission to the elderly Children’s Birthday Gatherings and SARS-CoV-2 Infection in Grandparents jamanetwork.com/journals/jam...

Kuwait says it intercepted Iranian ballistic missiles and drones entering its airspace. Iranian drone strikes hit military facilities and critical infrastructure, including a power and water desalination plant, causing fires, damage to power generation units, and injuring several soldiers.

⚡️ The United States Central Command (CENTCOM) announced that a new round of attacks against Iran has been carried out.

Sirens in Kuwait. Air defense is active

⚡️ Explosion heard in Sirik, bushehr, Bandar abbas and Qeshm

Explosions reported from Kuwait.

🇺🇸⚡️🇮🇷Footage of U.S. strikes against Lar, Fars Province.

Now

Iran struck U.S. military facilities in Bahrain, IRGC claims. According to IRGC, a U.S. drone storage facility was hit, and the main artificial intelligence center was completely destroyed.

🇺🇦⚡️🇷🇺—At this moment, more than 400 drones are reportedly heading toward Russia to strike military and economic targets. Support us❤️ : ko-fi.com/osintradar445

🇺🇸⚡️🇮🇷—The United States is striking an underground ballistic missile base in the city of Yazd, Iran. This is being done to protect global trade from terrorism and to ensure the security of the Strait of Hormuz, according to journalist Amjad Taha from the UAE.

New thing from midwest Loser_Theorem Cc @ryanhisner.bsky.social check it out He just published four songs one better than the other youtu.be/QVkbCNqgEqU?...

🇺🇦 According to the General Staff of the Armed Forces of Ukraine, a Svetlyak-class patrol ship (Project 10410) was damaged in Kerch, in the occupied Autonomous Republic of Crimea.

In the past two days very little sequences uploaded if not for a big recent batch from Costa Rica that unexpectedly sees QY.2.1 (435S) and QF.2.1 (641K) leading over all the other lineages including a PY.1.1.1 branch still circulating at good level there.

💈 Il caso Roggero non è legittima difesa. La sentenza dei giudici è giusta e corretta www.valigiablu.it/caso-roggero...

🇺🇦Overnight, Ukrainian forces reportedly struck another 12 Russian vessels in the Black Sea.

💈 Un’inchiesta di BBC Eye in India ha svelato la presenza su Instagram di annunci a pagamento che promuovevano video di abusi su minori e stupri, con link di acquisto verso canali Telegram. L'indagine riapre il dibattito urgente sulla sicurezza e sul reale controllo dei contenuti sui social

BREAKING NEWS A Syrian military source: “The Iranian strike that targeted Syria hit an uninhabited desert area and did not reach al-Tanf.” The source added that no U.S. forces have been present in the al-Tanf area since their withdrawal last February.

🇺🇦 Evacuation from Kostiantynivka has become impossible: leaving the city is now only possible on foot, according to the head of the press service of the Donetsk regional police.

UKMTO WARNING 088-26 - ATTACK

Five bridges in Khamir County, Hormozgan Province, were struck in U.S. airstrikes Thursday, a senior U.S. official told the WSJ, saying the strikes aimed to disrupt supply routes to Bandar Abbas, a key IRGC naval base near the Strait of Hormuz. iranwire.com/en/news/155077

Kuwait says Iran attacked a power and water desalination plant, causing widespread damage to the station. The country relies heavily on desalination for drinking water, so any disruption poses a serious threat. apnews.com/article/iran...

BREAKING NEWS: Ukrainian President Zelenskyy said Ukraine’s Security Service (SBU) has destroyed a Russian Tu-95 strategic bomber at the Engels air base.

Just throwing this out there in case someone might be interested in testing the BA.3.2 ORF6, which might give us additional understanding of its penchant for kids, or ORF6:P57S in a D61L context, which could provide insight into the dynamics of chronic infections. 15/end

But where reversions are rare or difficult, nearby mutations can often compensate for the harmful effects of the original mutation. I think one example of this is likely ORF6:P57S. It's the only common ORF6 substitution that's distinctly overrepresented in chronic-infection sequence. 12/15

So if ORF6:D61L is a harmful mutation, why doesn't it revert? Essentially, it can't. It's a 3-nuc mutation & L61D would require two extremely rare nuc mutations. I've seen just one case of a ORF6:L61D reversion that appeared genuine. 11/15

I suspect the ORF7a:V82A mutation in Delta did something similar, which is why it reverted so often in chronic Deltas. It's rare that mutations like this are tested though, so major props to @systemsvirology.bsky.social & co-authors for doing this work. 10/15 pubmed.ncbi.nlm.nih.gov/38397027/

Remarkably, the mutation with the highest reversion rate of all, ORF7a:H47Y, was the subject of a study by @systemsvirology.bsky.social @SystemsVirology, who found that it cripples ORF7a's ability to reduce MHC-I surface expression (which CD8 T cells use to bind to & kill infected cells). 9/15

In some cases, these mutations may be compensatory for deleterious mutations present in the infecting variant. I think this is the case with many of the reversions that are extremely common in chronics. Mutations w/the highest reversion rates in chronic infections (EPCI) are shown below. 8/15

#2: Mutations overrepresented in chronic seqs (relative to circulating seqs) are almost certainly functionally meaningful—e.g. Ab evasion, T-cell evasion, or adaptation to a tissue type. See new preprint by me, @darrenmartin.bsky.social, & Ravi Gupta on this. 7/ www.biorxiv.org/content/10.6...

So we don't know what BA.3.2's ORF6—with its 5-AA extension—can do, but we do know it might be very different from the prevailing ORF6:D61L variety given the large and opposing effects of adding or removing just a 2-AA extension. 6/15

Some sarbecos (e.g. SARS-1) have a 2-AA extension on ORF6. Removing the extension from SARS-1 enormously increases its NPC binding, but adding it to SARS-2 ORF6 slight increases its binding. So we know C-terminal extensions can have a large effect, but in complex, hard-to-predict ways. 5/15

All of the ORF6:52-61 residues are highly conserved in sarbecoviruses, with the exception of Q56. Mutation experiments suggest M58 is crucial & that more negative charge = higher binding to the nuclear pore complex (NPC). 4/15

ORF6's tail is key for binding to the nuclear pore & shutting it down. Negative charge (D's & E's) is crucial for this, which is why loss of the C-terminal D inhibits its function. BA.3.2 lacks D61 but adds an E three sites down. Might this restore ORF6's powers? Or does it further inhibit it? 3/15

First, BA.3.2—saltation variant from ~3-year chronic infection—is the first variant since BA.5 to lack ORF6:D61L. Instead, it gets D61H + an LNEQT extension. This has been entirely overlooked, including by me. Does this restore ORF6's powers—or further cripple them? 2/15

ORF6 is a SARS-2 protein that shuts down traffic between the nucleus & cytoplasm in host cells, inhibiting host mRNA export & immune responses. But in all variants since early 2023, ORF6's abilities are hampered by the ORF6:D61L mutation. Two newish ORF6 observations.... 1/15

Tek et al. report chromosome-scale genome assemblies for four duckweed species; comparative phylogenomics with land plants and the seagrass Zostera marina reveals a coherent, non-random program of gene loss. 🔗 doi.org/10.1093/gbe/evag163 #genome #societyjournal

Hong Kong wave is further with al indicators uptrending The number of outbreaks concentrated in long term care facilities is clearly showing how the new 420N variants PQ.16.1.1/SV* SZ.3.1 circulating there are very efficient in evading the locally build immunity www.chp.gov.hk/files/pdf/co...

(2/3) NSW COVID-19 Whole Genome Sequencing: 16 July 2026 🔸Last updated: 4 July 2026 🔹 NB.1.8.1: ~62% (estimated) 🔹 BA.3.2: ~20% (estimated) 🔹 XFG: ~13% (estimated) 🔹JN.1: ~5% (estimated) @NSWHealth

Chandipura virus confirmed in seven children in Gujarat, India, with three deaths and four on ventilator support https://beaconbio.org/en/report/?reportid=5f5a52b1-a20c-414e-a71b-ff3d6cfa1199&eventid=5aa87f7e-5b22-409e-900f-7c922d2e5a60&utm_source=bluesky&utm_medium=social&utm_campaign=socialpost

How do cells "hibernate"? Deep-sea archaea (100°C, 40 MPa) hold the answer. Scientists identified a protein controlling ribosome dormancy, also found in human gut archaea. Nature Communications #Archaea ↘️ www.pasteur.fr/en/press-are...

The work established the structural blueprint for polymerases across non-segmented negative-strand RNA viruses. Structure of the L Protein of Vesicular Stomatitis Virus from Electron Cryomicroscopy: Cell www.cell.com/cell/fulltex...