Chris Tomkins-Tinch

[Chris Tomkins-Tinch @tomkinsc]

When someone has COVID-19 twice, months apart, is it a reinfection or recrudescence of the original infection? In this case report we use genomic data to discriminate between the two:
https://t.co/nG6HyZ0n9n

[👩‍💻 Paige Bailey @DynamicWebPaige]

👩‍💻 If this is what ChatGPT is like (a variant of InstructGPT), then GPT-4 is going to be *bonkers*.

👇🏻A thread of my favorite examples of ChatGPT, for source code-related tasks:

https://t.co/GPvNDXZVd0

[Melis Anahtar @melisanahtar]

Got a + SARS-CoV-2 nucleic acid amp test (NAAT) result ≥45 days after an initial + result? How do you distinguish persistent RNA detection from genuine reinfection?

Read our new paper (big collab w/ @mghid, @mghpath, @sabetilab 🥳) in @cidjournal: https://t.co/SuuWK0Q2iQ
👀🧵👇

[Chris Tomkins-Tinch @tomkinsc]

Lesson here: important for families to be COVID-careful when students are home from school, and for schools to be vigilant at the start of terms. Prob also wise for schools with testing programs to continue them over break & maybe offer extra tests for contacts of students.

[Chris Tomkins-Tinch @tomkinsc]

Another thing this plot tells us is that just because school's out, transmissions chains to students do not necessarily stop. We found case clusters before and after winter break (top cluster), with a cryptic transmission chain of 2-3 hops connecting them.

[sabeti_lab @sabeti_lab]

We characterized the viral lineage B.1.429.1, a descendant of a former Variant of Concern, and considered sociobehavioral and viral phenotypic factors at play in its rapid expansion. (8/x)

[Chris Tomkins-Tinch @tomkinsc]

The cases linking the clusters are unknown to us & so un-sequenced—could be people outside the school community connected to those who are, or folks from the university who spent time together over the break.

[Chris Tomkins-Tinch @tomkinsc]

@sabeti_lab @ColoradoMesaU @fathominfo @EmilyAnthes What did we find? Check out the thread below for highlights and the linked pre-print for details. https://t.co/8q2bp9s6Kz

[sabeti_lab @sabeti_lab]

Excited to share our preprint, https://t.co/o3EBzC7LWf. Collab led by @PetrosBrittany, Jillian Paull, @tomkinsc, & @technologybryn with @ColoradoMesaU, @PardisSabeti, @LubanLab, @fathominfo, @degreeanalytics & more (1/x).

[Chris Tomkins-Tinch @tomkinsc]

🏫School is in session: When SARS-CoV-2 hits a university community, does it spread like wildfire? Are some more likely to catch it than others? @sabeti_lab, @ColoradoMesaU & @fathominfo have been working together to find out so students can be better protected in the future 🧵…

[sabeti_lab @sabeti_lab]

Excited to share our preprint, https://t.co/o3EBzC7LWf. Collab led by @PetrosBrittany, Jillian Paull, @tomkinsc, & @technologybryn with @ColoradoMesaU, @PardisSabeti, @LubanLab, @fathominfo, @degreeanalytics & more (1/x).

[Chris Tomkins-Tinch @tomkinsc]

@sabeti_lab @ColoradoMesaU @fathominfo @EmilyAnthes We looked at a ton of anonymized info for greater understanding: 1) dates+attributes of cases; 2) viral genomes from sequenced diagnostic tests; 3) viral load & sequence data from residential wastewater, and 4) contact tracing data, collected traditionally+digitally.

[Chris Tomkins-Tinch @tomkinsc]

I'm grateful for the mentorship of @PardisSabeti, @bronwynmacinnis, @DannyJPark, @glipsnort, and many others in the @sabeti_lab, as well as Stuart Levitz and @LubanLab of @umassmemorial.

[Chris Tomkins-Tinch @tomkinsc]

Does that make sense clinically? An IgG assay for anti-SARS-CoV-2 antibodies was negative at the start of the second infection. We speculate lack of antibodies made the patient susceptible to reinfection. All data taken together, we identified this to be a case of *reinfection*.

[Chris Tomkins-Tinch @tomkinsc]

It was enabled by contextual data contributed by so many to @NCBI GenBank in connection with efforts and encouragement from @CDC_AMD.