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Ganesh Kadamur Profile picture
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20 Apr, 6 tweets, 5 min read
A #virology evolutionary hypothesis on this one - it is *likely* less virulent, more transmissible than B.1.1.7/B.1.617

Less mutations head to head in multiple ORFs, yet seemingly rapid increase in prevalence in face of competing B.1.617.

Thoughts? @thattai @dylanhmorris
Mutations in B.1.1.7 and B.1.617, both well established, lineages would have been fixed for some benefit. For nature to choose *not* to fix them in B.1.618 implies some benefit of losing them. Of course, protein allostery incredibly hard to predict a priori, but Occam's razor..
..along with the increasing prevalence of B.1.618 in West Bengal while B.1.617 also expands would suggest increased transmissibility and lower virulence. Immune escape propensity is a different issue altogether of course.

Full list of mutations in all 3 strains - outbreak.info/compare-lineag…
Castle in the sky hypotheses time, would love to hear more thoughts on this

@HarmitMalik @arambaut @pathogenomenick @klausenhauser @BallouxFrancois @macroliter @iskander @ewanbirney @Merz

An alternate possibility would be that this has a longer pre-symptomatic period vs B.1.617, but that seems less plausible - after all, no documented evidence of this happening (yet)

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Ganesh Kadamur Profile picture
20 Apr
India's 2nd covid wave still rising. However, some states have been mostly spared *seems like* so far - Tamil Nadu, Telengana specifically. Undercounting yes, but no huge reports of hospitals overburdened (yet). However, vaccine wastage also huge here

businesstoday.in/current/econom…
Events like death of a famous loved actor Vivekh haven't helped at all, though docs have said he had preexisting conditions.

Any wastage is unacceptable in current circumstances, let alone 10%+. We need to do better.
Some of this is vaccine hesitancy I understand from social media (WhatsApp groups I'm part of, ears on ground from family, one on one conversations with family friends etc). The state, and central, govt seem barely interested in extensive publicity campaigns to counter.
Read 12 tweets
Ganesh Kadamur Profile picture
20 Apr
@sujithrao @vinodscaria @bani_jolly @mercy_rophina @Arvinden3 @AfraShamnath @SridharSivasub3 @PrinSciAdvGoI I did oversimplify that bit, my apologies. I'll explain.

By virulent, I meant disease causing ability. So less virulent=less severe disease. Why did I say that? A virus just wants to survive and transmit. It needs hosts to do so, can't do it on its own. (1/)
@sujithrao @vinodscaria @bani_jolly @mercy_rophina @Arvinden3 @AfraShamnath @SridharSivasub3 @PrinSciAdvGoI Consequently, something that starts out as very virulent will, as it mutates and "evolves", a variant *can* emerge that transmits equally/better but causes less severe disease, thus allowing it to continue "living" and spreading and do it "better"

Now, there's one other way (2/)
@sujithrao @vinodscaria @bani_jolly @mercy_rophina @Arvinden3 @AfraShamnath @SridharSivasub3 @PrinSciAdvGoI specifically in this context, we ought to remember that CoV2 has a pre-symptomatic period - where you have caught the virus and it is in the body and is multiplying, but your body has not "reacted" visibly to it - ie., symptoms like fever etc

so another way for a variant to (3/)
Read 6 tweets
Ganesh Kadamur Profile picture
19 Apr
It is indeed impossible for anyone to predict how the 2nd wave in India will play out, when it'll peak etc.

Worth trying still, not so much for scare mongering but for maybe some idea of what's ahead. Brazil had a similar catastrophe, except earlier, and can be instructive Image
I use Brazil because it's similarly developing country, vast tropical climate, but also because the peaks and interval between waves has some uncanny similarities, especially in deaths
Wave 1 - peak 6Sep20 IN, 9Jun20 BR (~3mo)
Start wave 2 - 6Mar21, 9Nov20 BR (~3mo) Image
I'll caveat the comparison strongly as multiple differences - potential strain, vaccination much higher in India than Brazil was in Nov, climate etc.

But healthcare systems being saturated is similar. India is now *maybe* where BR was ~Feb'21

Read 14 tweets
Ganesh Kadamur Profile picture
28 Mar
Reflecting on some career panels I participated in, networking was the buzzword that came up repeatedly. But what IS networking? How/why to do it?

A thread on what/how with some personal examples; I'll get to the why later (1/)

@AcademicChatter #careers #phdlife #altac
Networking, to me, most simply is making new *friends* who will _eventually_ help you *professionally*. It is those you you share something in common professionally (same industry, same kind of work etc) in contrast to personally (went to same college, like same music etc) (2/)
It takes a while to become good friends with someone. It's the same w/ networking - it takes time to build that bond, and need to be patient. One asks favours only from friends they know well - same for your networking connections. Start early, don't wait till you need a job (3/)
Read 26 tweets
Ganesh Kadamur Profile picture
26 Mar
While this is indeed a hugely mutated form of #SARSCoV2 when compared to the "original" sequence from the Wuhan patient, its a bit exaggerated to say this as evidence of any evolutionary rate. Tanazania, and all Africa's, level of infections is likely far underdetected after all
With little understanding of the level of underdetection, could be easily be a couple immunocompromised hosts + few transmissions. Or The 18907 V->F is in nsp14 and might impact Rdrp proofreading. All said, any claims on immune evasion/transmissibility are only hypotheses now
However, such data also shows the power of genomic sequence surveillance as much as possible to both understand the underlying biology and prepare for potential public health ramifications.

Its also easily misused for fear mongering - one thing to stay guarded against.
Read 6 tweets
Ganesh Kadamur Profile picture
26 Jan
Colour me biased but very little has been said about India and it's absolute squashing of (reported) cases in media overall, Western and otherwise, afaik. It's quite something for a densely populated state to reach 100k/day then go down this well, clearly lots to learn (1/)
Sure there's underreporting, but if you argue that, then the peak looks even worse which makes this even more amazing IMHO. No more huge reports of any hospitals being stressed, so this just has to be real (2/)
First hand exp, can say people back on streets, shops open - many offices still shut, but public transport ~normal crowds yet no resurgence. Winter in the north is as cold as UK, yet no resurgence there either, so not just weather (3/)
Read 20 tweets

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