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babar Profile picture
babar
@babarlelephant
φ(ab)=φ(a)φ(b)
Jun 21, 2022 • 5 tweets • 3 min read
First preprint with @Engineer2The @Drinkwater5Reed @franciscodeasis on our dive into early Covid cases, focusing on sequences. zenodo.org/record/6672912

We found some raw reads unpublished as sequences (academic.oup.com/cid/article/71… ) and that Beijing's 1st case was earlier than thought Image Overall we get 19 sequenced patients with onset in 2019, 16 of which are linked to the Huanan market.
We could then obtain a reasonable consensus genome for each of these early patients, likely representing the haplotype at the time of onset. ImageImage
May 25, 2022 • 4 tweets • 2 min read
The MVA-BN monkeypox vaccine en.wikipedia.org/wiki/Bavarian_… is attenuated (passaged in chicken cells) and replication incompetent in human cells. But in the same passages they obtained MVA-I721 and MVA-572 that are replication competent and genetically identical to MVA-BN 🤔 Image It is a vaccinia virus (strain Ankara, worth to mention as there is a lot of diversity in VACV), 97.6% identity both to monkeypox and variola virus on most of the genome. And it is MVA-I721 which replicates well in human cells.
Jul 25, 2021 • 5 tweets • 3 min read
An update on my partial RdRp #sarbecovirus tree. This is now the region 15000-16000 with many smaller sequences.
nextstrain.org/community/baba…
Once sample is collected they do a PCR, if positive they sequence the region 15300-15700, if interesting they try to sequence the whole genome Species: Rhinolophus, 9 Hipposideridae, 2 Human, 2 Civet, 3 Pangolin, 1 Chinese badger, 2 Vesper, 1 Molossidae.

No rhinolophids in America. In other countries rhinolophids were sampled and were negative to CoV or sarbecovirus. Turkey unsampled, there are sarbecoviruses there!
Mar 29, 2020 • 32 tweets • 17 min read
La propagation de l'épidémie en France.

🔹On constate deux importations d'Italie.
🔹La seconde plus tardive en Alsace a bénéficié d'un événement de super-spreading lors de la réunion évangélique.

#phylogenetic #SARSCoV2 #covid19 @nextstrain nextstrain.org/ncov?c=gt-nuc_… Image Pourquoi j'affirme que le sous-arbre vert est celui de Mulhouse : les dates, les lieux, l'homme de 86 ans à Thise nextstrain.org/ncov?s=France/… macommune.info/coronavirus-10…
Le fait qu'il y a deux gros foyers épidémiques bien identifiés en France : IDF et Alsace.
Mar 15, 2020 • 14 tweets • 6 min read
Deux versions (donc deux importations) de SARS-CoV-2 se baladent en Alsace fin février : celle du sud Espagne et celle d'Allemagne-Italie-Suisse-Pays-Bas.
0.05% de différence entre deux donc peu de chance de corréler à une différence de virulence ou contagiosité. @Brevesdepresse Si on regarde les séquences des pays voisins de la France on couvre une bonne partie de l'arbre. Il y a eu une petite dizaine d'importations épidémiques en Europe et certainement plus que deux d'entre elles circulent en France. nextstrain.org/ncov?c=country…