🔴Transmissibility or Virulence : What should really worry us ?
Since these two have been widely discussed, given #omicron is around. A short explainer 👇.
3 plots below - from ~2x of Rt value and 1/2 of hospitalization rates (less virulent) to basal value (~ Delta wave)
Rt is the effective reproductive no.
One could clearly see why 2x Rt would create a sharper and ⏫rate of hospitalizations.
For a less virulent and highly transmissible variant, assuming 1/2x hospitalization rate, this would still create a significant wave of hospitalizations.
A much detailed mathematical basis to this was discussed in the past by @AdamJKucharski
Why is this important to discuss ?
The early and preliminary estimates of Rt from #Gauteng is now available , thanks to analysis from @lrossouw . See the detailed analysis at unsupervised.online/static/covid-1…
The context and Rt values for previous waves are also put in context.
What can we do ?
▶️ Vaccinate 💉all the remaining and eligible pop.
Especially the high risk groups (40y+ & people with comorbidities) without fail and urgency.
▶️ Ensure we diligently embrace 😷#masks #SocialDistancing and 🪟 #ventilation
▶️And of-course 💉💉💉 boosters (when available). An update on the need given the context of growing evidence on #omicron is here by @neutranino:
thehindu.com/news/national/…
The numbers (2x, 1/2x etc) are only descriptive purposes to make the point and may not reflect the estimates we might get for omicron. Looking forward to (re)estimates over the next couple of weeks.
Also to highlight the need to protect #HealthcareWorkers , in the case scenario of a sharp peak over a short period of time. A major determinant of available capacity during a wave would indeed be the availability of Healthcare workers to offer care.
What is the relation between Hospital load and increased COVID-19 related mortality ?
What is the relation between case load and excess deaths ?
An interesting analysis from #Israel 🇮🇱nature.com/articles/s4146…

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More from @vinodscaria

30 Nov
Scotland outbreak cases had no apparent travel history to Southern Africa.
theguardian.com/uk-news/2021/n…
Germany reports case of Omicron variant in Leipzig with no travel hsitory to Southern Africa
freepressjournal.in/world/germany-…
Read 4 tweets
29 Nov
SARS-CoV-2 Variants and RT-PCR
Can RT-PCR Detect Omicron ?
A short thread on the topic. 👇
RT-PCR is a sensitive molecular method widely used for the detection of SARS-CoV-2 in biological samples. This is based on the principle that short pieces of DNA (aka primers) can specifically target DNA/RNA and amplify them using a polymerase protein
Typically COVID-19 RT-PCR kits use 2 or more sets of primers which target the virus nucleic acid at 2 or more genes/sites in the genome. This is to improve the specificity of the detection. Combinations between N, E, RdRP and S genes are typically used.
Read 10 tweets
25 Nov
What do we know about the B.1.1.529 variant of SARS-CoV-2 with a very large number of mutations
An updated thread on emerging evidence. Image
B.1.1.529 is a newly designated variant of SARS-CoV-2 github.com/cov-lineages/p…
This would not have been possible without the exemplary work of researchers in Africa who have sequenced and deposited the genomes in public domain which forms the basis of this variant designation.
The lineage (variant) is characterized by 32 conserved spike mutations A67V Δ69-70 T95I G142D/Δ143-145, Δ211/L212I ins214EPE G339D S371L S373P S375F K417N N440K G446S S477N T478K E484A Q493K G496S Q498R N501Y Y505H T547K D614G H655Y N679K P681H N764K D796Y N856K Q954H N969K L981F
Read 28 tweets
24 Nov
Real-world data on effectiveness of BBV152 / Covaxin whole inactivated #COVID19 vaccine against symptomatic infection
👥Healthcare Workers at @aiims_newdelhi
🗓 Coincided with the 2nd wave in #Delhi majorly driven by VoCs
thelancet.com/journals/lanin…

#MedTwitter #vaccines #India
Adjusted effectiveness of BBV152 against symptomatic COVID-19 after 2 doses adm at least
🔸️14d before testing was 50% (95% CI 33–62; p<0·0001).
🔸️28d before testing was 46% (95% CI 22–62) 
🔸️after excluding previous COVID19 cases, 14d before testing was 47% (95% CI 29–61)
In summary
🔸️Vaccine effectiveness requires at least 2 doses and 14 days after 2nd dose

What this means for #PublicHealth
🔸️ Underscores the need for completing vaccine schedule of 2doses
🔸️ Continued non-pharmacological measures in the face of a wave of infections
Read 4 tweets
3 Nov
Insights on the recent wave of COVID-19 infections in @Singapore
The present wave in Singapore is of interest since a significant large proportion (82.7%) of population has received 2 doses of #COVID19 #vaccines but nevertheless have a wave of infections and deaths.
With respect to COVID-19 variants and VoCs, clearly Delta (and 2 prominent sublineages AY.23 and AY.23.1) dominate the present wave of infections.
Data: @DiseaseOutbreak
There are some interesting insights, thanks to the data made available at data.gov.sg
While on first look there is a significant number of cases spread across all age-groups.
The community cases are largely dominated by the younger age-groups (59 years and above)
Read 8 tweets
20 Oct
What do we know and don't about the Delta sub-lineage AY.4.2
ℹ️ AY.4.2 is a sub-lineage Delta (B.1.617.2) in the UK which has shown consistent increase over the past few months and has caught attention.
Plot: Sanger COVID-19 Genomic Surveillance Dashboard covid19.sanger.ac.uk/lineages/ Image
The background:
Delta had significant advantage over other lineages, in almost all regions, practically eliminating all other lineages as they spread widely.
The continued evolution of delta provided a number of sublineages
There are now ~55 sublineages (AY.1 - AY.41) of Delta
Some of the AY.x sublineages have geographical preponderance, due to mutations present at the time of introductions. For example, UK has a AY.4 sublineage. More about the lineages and distribution is available at cov-lineages.org/lineage_list.h… Image
Read 9 tweets

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