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Moreno Colaiacovo Profile picture
Moreno Colaiacovo
@emmecola
Bioinformatics l Web development | Data analysis - I work as an external consultant for the JRC. All views expressed are my own.
Jul 23, 2023 • 6 tweets • 2 min read
It took me some time to read all the Slack conversations between the #ProximalOrigin authors (not just the cheery-picked quotes), but it was a useful exercise.

It showed in real time how their thinking evolved with new evidence, as the authors themselves have been saying. 1/ So now I have no doubt that they did change their mind because of new information, i.e. #pangolin CoVs with similar RBD and bat virus with putative insertions in the FCS spot.

Of course one could wonder if their assessments were correct, but that's a separate issue. 2/
Apr 11, 2023 • 9 tweets • 3 min read
"The proximal origin of SARS-CoV-2" will probably be one of the most debated and criticized papers of all times. @edwardcholmes has shared the responses to the reviewers, which is interesting especially because some critics said it wasn't peer reviewed. 1/
documentcloud.org/documents/2373… Reviewer #1 would like to know the authors' view on the possibility of a lab leak of a natural virus. Their response clarifies why they believed no lab scenario was plausible: the opportunities for animal-to-human spillovers are more frequent. 2/ Image
Oct 22, 2022 • 6 tweets • 2 min read
Ok guys, for me the #OriginOfCovid debate has come to an end. After I changed my mind on the most probable origin, Twitter interactions have become more difficult for me. 1/ When I was on the lab leak side it was much easier. The zoonosis proponents have never insulted me, the worse thing they did to me was blocking me. But in the last few months, debating this topic on Twitter has become less and less pleasant. 2/
Oct 22, 2022 • 6 tweets • 2 min read
As I always do, I tried to keep an open mind about this recent preprint. I also invited people to avoid insults and read the paper before criticizing it.

I read several technical comments from experts, and unfortunately it didn't end well for the authors. 1/ This is the most obvious mistake, which IMO invalidates the conclusion of the paper. The restriction enzymes that have been analysed cut outside their recognition site, which means that cloning strategies using them remove the sites in the final product 2/
Oct 21, 2022 • 8 tweets • 4 min read
I share this preprint to encourage all virologists, bioinformaticians and molecular biologists to address it and search for flaws. I know emotions run high, but please try to be civil and express your criticisms as clearly as possible for the general public. 1/

#OriginOfCovid I will post the most interesting responses that I found on Twitter, and update the thread whenever new comments are posted. Here's @BallouxFrancois endorsement. 2/
Aug 19, 2022 • 17 tweets • 13 min read
C'è molta curiosità intorno a @PossibileIt e al suo programma per le #Elezioni2022, ma siccome molti sono intimoriti dal file PDF di 95 pagine ho deciso di raccogliere in questo thread i punti principali. 1/

#PossibileItalia

possibile.com/possibile-ital… CLIMA

➡️ 10 GW di #EnergiaRinnovabile installati ogni anno (siamo fermi a 0.85/anno) ☀️
➡️ Manutenzione straordinaria della rete idrica 💧
➡️ Stop al consumo di suolo, più alberi nelle città 🌳
➡️ Investimenti su trasporto pubblico, ciclabili e mobilità elettrica 🚲

2/
Mar 7, 2022 • 10 tweets • 3 min read
Breve thread per gli italiani confusi dalle dichiarazioni di #Palù, apparse negli stessi giorni in cui la stampa internazionale sta invece rilanciando l'ipotesi wet market per l'origine di SARS-CoV-2. 1/ Palù si riferisce a un suo paper pubblicato due settimane fa in cui segnalava la presenza di una particolare sequenza del virus (quella che codifica per il Furin Cleavage Site, FCS) in una vecchia sequenza brevettata da Moderna per la cura del cancro. 2/
Mar 1, 2022 • 21 tweets • 7 min read
I've had a closer look at the preprint recently published by @MichaelWorobey and others. Everybody knows that I have been skeptical about the market origin hypothesis and I sympathize with many "lab leakers". However, this time I am quite impressed. 1/
zenodo.org/record/6299600… Since the beginning of the pandemic, we have been struggling to get access to relevant data from China (both from the labs and the market). But these guys made a tremendous effort to extract as much as info as possible from imperfect data, and I think they did a good job. 2/
Feb 22, 2022 • 7 tweets • 4 min read
È uscito su @FrontVirology un articolo firmato da Giorgio #Palù dove si ipotizza che il sito di taglio della #furina presente in SARS-CoV-2 possa essere stato ottenuto in laboratorio. 1/
frontiersin.org/articles/10.33… L'ipotesi parte dalla scoperta di una sequenza brevettata da #Moderna in cui si trovano 19 nucleotidi identici a quelli che nel virus codificano per il famoso furin cleavage site (FCS). 2/ Image
Dec 28, 2021 • 10 tweets • 4 min read
Mi sono divertito ad usare il tool online di @bmj_latest per calcolare la capacità predittiva di due test #antigenici disponibili in commercio: un #tampone nasale e un salivare. 1/ Il produttore dichiara per il tampone nasale una sensibilità del 95.4% e una specificità del 99.4%. I valori per il test salivare sono più bassi: rispettivamente, 90.1% e 99.3%. 2/
Dec 12, 2021 • 6 tweets • 2 min read
Big news from China on the search of the #OriginOfCovid - Head of Chinese WHO team attacks @MichaelWorobey paper: "unscientific to conclude that some early cases living close to the market was proof that it was the origin of the community transmission." 1/
archive.md/ybb2a "Liang said Worobey did not verify the identity of a patient featured in The Paper’s video report. He said the first identified Covid-19 case did visit the hospital between December 6-8, and was accompanying a family member for a tooth extraction." 2/
Dec 8, 2021 • 6 tweets • 3 min read
Someone found in a #Moderna patent from 2017 a short nucleotide sequence that is identical to the one encoding for the Furin Cleavage Site in SARS-CoV-2. While this may seem suspicious at first sight, I'll try to explain why there's "nothing to see here". 1/ First of all, the nucleotide sequence is really there. It is located in sequence 11652 from patent US 9587003, position 2733-2751 (revers strand). The Genbank ID is KH664781. 2/
ncbi.nlm.nih.gov/nuccore/KH6647…
Oct 24, 2021 • 25 tweets • 18 min read
Per chi volesse approfondire i temi trattati nel servizio di #PresaDiretta di ieri sera, ho raccolto in questo thread le fonti e i documenti principali citati in trasmissione. 🧵1/ Cominciamo dalla missione dell'#OMS a #Wuhan, all'inizio di quest'anno. Qui trovate il rapporto finale che considera "estremamente improbabile" l'incidente di laboratorio. 2/
who.int/publications/i…
Aug 25, 2021 • 11 tweets • 4 min read
One last thread on the origins of #SARSCoV2 before the upcoming publication of the US intelligence report. First of all, there are two things that might be even more important than the origin itself: research ethics and scientific debate. 1/ Since the beginning, some scientists working in Chinese institutions haven't been fully transparent. The history of #RaTG13 and the issues with its sequencing data, the miners pneumonia, the missing database, the pangolin CoV data. Hiding info, playing with words. Bad science. 2/
Apr 5, 2021 • 16 tweets • 10 min read
THREAD - What happened at the Huanan #seafood market?

The @WHO report is quite clear on this point: #SARSCoV2 might have jumped from a wild animal sold in this market and maybe other markets in #Wuhan. But what do we know exactly? 1/15

#originsofSARSCoV2 Image After all this time, the Huanan seafood market still remains the main suspect for a simple reason: most of the early cases had visited at least one market in Wuhan city, and several of them visited the Huanan market. 2/15 Image
Feb 21, 2021 • 11 tweets • 5 min read
Tra le #mutazioni del virus che preoccupano di più ci sono la #N501Y e la #E484K.

La prima permette a SARS-COV-2 di legarsi meglio al recettore ACE2, in altre parole i virus con questa mutazione riescono a entrare più facilmente nelle nostre cellule. 1/ Variante inglese 🇬🇧 (B.1.1.7), sudafricana 🇿🇦 (B.1.351) e brasiliana 🇧🇷 (P.1) hanno tutte quante la mutazione N501Y.

Probabilmente, è proprio per questo motivo che queste varianti tendono a essere più contagiose. 2/
Dec 26, 2020 • 5 tweets • 3 min read
Question for bioinformaticians! Believe it or not, the first genome of bat virus #RaTG13 had some nucleotides that were supported by zero reads: in other words, the genome didn't match the sequences that were used to assemble it. How is it possible? 1/
#originsofSARSCoV2 Assemblers are computer programs, they do not "invent" nucleotides. So, what happened here? My explanation was that this genome was assembled using other reads, maybe in addition to the ones that were uploaded. 2/
Nov 20, 2020 • 8 tweets • 4 min read
Some "conspiracists" always get it right!

Conspiracist, January 2020: "#RaTG13 virus looks like BtCoV/4991 described in an old paper that you didn't cite!" 📄

Average scientist, January 2020: 😴

Shi Zhengli, July 2020: "Yes, it was the same virus."

#SARSCoV2 #SARS2origins

1/ Conspiracist, May 2020: "Look, these sequences in database are dated 2017/2018. So you didn't sequence RaTG13 this year, as you wrote in the paper!" 🔬

Average scientist, May 2020: 😴

Shi Zhengli, July 2020: "Yes, actually we got the sequence in 2018."

2/
Sep 13, 2020 • 6 tweets • 4 min read
La virologa cinese #LiMengYan dice che #SARSCoV2 è stato creato in un #laboratorio di #Wuhan. Senza vedere le prove (che lei sostiene di avere), mi risulta difficile credere alla sua tesi. 1/
nypost.com/2020/09/11/chi… La scienziata, infatti, sostiene che #SARS2 sia una #chimera dei virus dei #pipistrelli ZC45 e ZXC21.

Ora, è vero che a Wuhan facevano chimere a scopi di ricerca, ma questi due virus sono troppo diversi da SARS2 per essere i suoi antenati diretti. 2/

Apr 29, 2020 • 7 tweets • 3 min read
Il modello di @istsupsan che ha guidato le decisioni del governo sulla fase 2 è un modello SIR stocastico strutturato per età. Uno dei punti di partenza è questa tabella, che quantifica i contatti medi degli italiani in base a età e luogo del contatto. 1/ La suddivisione dei lavoratori in base al settore di attività (es. edilizia, manifattura) si basa su dati INAIL. Il modello fa molte assunzioni: ad esempio ipotizza che i contatti nel tempo libero passino dal 10% (dati Google) al 34% in caso di apertura di bar e ristoranti. 2/