Robert Gifford Profile picture
Mar 1, 2022 10 tweets 5 min read Read on X
*Tamanaviruses* - a primer (medium thread)
(1) Tamana bat virus (TABV) is a highly divergent #flavivirus that was isolated in 1974, from a bat trapped at the exit of Tamana cave, on the North slope of Trinidad's Mount Tamana. Image
(2) TABV was identified at the Trinidad Regional #Virus Laboratory (TRVL) as part of a post-war virus discovery effort lead by the Rockefeller Foundation.

The #Tamana cave system comprises several large limestone caverns and is a roost for several species of bat. Image
(3) Millions of bats fly out of Tamana cave exits to feed at dusk, making for an impressive spectacle.

Researchers at TRVL trapped #bats at cave exits, took samples from these bats and attempted to cultivate viruses. Image
(4) TABV was isolated from a moustached bat (Pteronotus parnellii).

Serological analyses performed at the time indicated that TABV was related to flaviviruses like yellow fever virus (YFV), but only distantly.

doi.org/10.4269/ajtmh.…
(5) TABV remained an enigma for decades.

In 1998 Kuno published electron micrographs of TABV propagated in Vero cells showing virus particles with the typical size and morphology of flaviviruses, but no virus sequences could be amplified via PCR.

doi.org/10.1128/JVI.72…
(6) When the TABV genome sequence was obtained in 2002 it only raised more questions.

Despite being closely related to the genus Flavivirus, and having a generally similar genome organisation, TABV is clearly distinct from other members of the genus.

doi.org/10.1099/0022-1…
(7) TABV is not only distinct in its phylogenetic placement, but also in other signature genomic traits such as nucleotide composition and GC content.

doi.org/10.1128/JVI.00… Image
(8) In recent years, however, advances in sequencing technology have lead to the identification of TABV-like viruses in a wide range of animal species, pictured below.

Host species include fish, insects, sharks and squid.

Some of these viruses have been isolated. Image
(9) These findings indicate that TABV is a representative of a novel, distinct group of flaviviruses ('Tamanavirus') that likely infects a broad range of animal species. Image
(10) In a recent paper, we reported 'genomic fossils' of tamanaviruses in tube-eye fish (Stylephorus), among other species.

This shows that these viruses - like other groups within the Flavivirus family - have ancient origins in the animal kingdom.

doi.org/10.1101/2021.0… Image

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More from @Paleovirologist

Apr 29
I created a GLUE project for the #H5N1 strain of influenza A, and used it to build outgrouped phylogenies for all eight segments of cattle isolates.

A few observations about these, which I'm sure are glaringly obvious to many, but still might be worth highlighting.
The chronograms - as viewable on NextStrain (left) - give the impression of structure but the phylograms (right) show very little genetic diversity within the cattle-associated clade. Image
Because there is so little structure and statistical support for branching relationships, I think its difficult to conclude much about what is going on in terms of cross-species transmission.
Read 6 tweets
Sep 19, 2022
This is a thread about how anyone can use publicly accessible sequence databases and free software to discover new things about #genomes, #biology, and life on earth.

#Bioinformatics #Genomics #Evolution #Science #MolecularBiology #DNA #Research #DataScience #LifeSciences Image
Genomes are absolutely loaded with complex information, most of which we still don’t understand.

Complete and near complete genome sequences are now available for many organisms.

However, decoding the information in these genomes remains a slow and difficult process. Image
A large proportion of most published genome sequences consist of DNA that is incompletely understood in terms of its evolutionary origins and functional significance. Image
Read 21 tweets
Feb 16, 2022
Short #Jingmenvirus primer - medium thread.

Jingmenvirus is a recently identified group of segmented RNA viruses that are phylogenetically linked to unsegmented flaviviruses. They appear to infect a wide range of animal hosts, including humans. Image
Jingmenviruses (JMVs) contain two #flavivirus-related segments, as well as additional segments of unknown origin. It is thought that JMVs evolved from unsegmented flaviviruses.
doi.org/10.1073/pnas.1…
The evolutionary significance of this shift to a segmented genome is unclear, but comparative studies of JMVs and flaviviruses may illuminating.
Read 15 tweets

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