Haogao Gu

Research Assistant Professor at HKU School of Public Health. Studying evolution and epidemiology of viruses, also the interactions to their hosts.

[Doherty Institute @TheDohertyInst]

We're #hiring! The Faculty of Engineering and IT are seeking a Research Fellow to contribute to a groundbreaking project on developing antiviral therapeutics for respiratory pathogens with pandemic potential using CRISPR-Cas13 gene-editing tools.
https://t.co/0Ry8S19qDf

[Haogao Gu @GuHaogao]

https://t.co/iUfg3o8kJR

[Haogao Gu @GuHaogao]

I truly thank Chase and love this collaboration, it was an amazing experience.

Note that in the analysis, we also estimate the fraction of nonsynonymous mutations that is beneficial in SARS-CoV-2, shown in Table 1. Hope these will also be helpful to related studies.

[Chase W. Nelson 倪誠志 @chasewnelson]

In a Matters Arising at @NatureComms, we discuss πN/πS for detecting within-host natural selection.

We also estimate the fraction of nonsynonymous mutations that is beneficial in SARS-CoV-2.

Grateful to @GuHaogao & @world_epidemic for the collab. 1/12 https://t.co/Odkej52wB2

[Leo Poon @world_epidemic]

A big thank to @EckerleIsabella, @DijkmanRonald and @ProfVolkerThiel. The @nidovirus2023 meeting went well. We from @HKU_SPH love it so much, great science, delicious food and a beautiful place!

[Nature Communications @NatureComms]

Within-host genetic diversity of #SARSCoV2 lineages in unvaccinated and vaccinated individuals

@GuHaogao @world_epidemic
#COVID19 #vaccines

https://t.co/y2KCvFjPce

[Matthew McKay @Matthew_R_McKay]

Research Fellow opportunity @UniMelb, @engunimelb, to work on computational methods/platforms to design next-gen vaccines & study viral evolution.

Collab with @TheDohertyInst, @UniMelbMDHS, @GarvanInstitute, Prof. @Row_Bull at @KirbyInstitute.

https://t.co/ircJUIRQ79

[Leo Poon @world_epidemic]

We deep sequenced >2800 Covid-19 patients, including those with a breakthrough infection, to study minor variants.

We observe that:
1. VOCs tend to generate more minor variants.
2. Vaccination does not increase non-silent mutations.

Now in Nat Comm.
https://t.co/nonbD3uywX

[Leo Poon @world_epidemic]

Does targeted travel restriction really work?

My experience: For the 50 imported omicron cases (random sampling) we sequenced in Nov/Dec 2021, only a few cases were from S. Africa. Many of them were from other counties in Asia, Africa, Europe, N. America.

[Haogao Gu @GuHaogao]

Description of the methods can be found in this [blog post] (https://t.co/9UQtCspa8m), Basically it accepts a BAM file (reads alignment) and a GFF file (region of interest) and returns Shannon entropy and Nucleotide diversity at haplotype level.

[Haogao Gu @GuHaogao]

When deep sequencing data is available, sometimes it is interesting to check the mutation diversity of reads within a specific genomic region (e.g., epitope region). I developed a light-weight tool for this purpose and usage can be found in https://t.co/lO9wepv6a7.

[Ben Cowling @bencowling88]

Perhaps most interesting observations for us were (1) the weaker T cell responses to a third dose in those primed with BNT162b2, and (2) the disparity between neutralizing antibodies (much higher with BNT162b2 booster) versus vaccine efficacy (seems similar between arms) (13/14)

[Haogao Gu @GuHaogao]

@richardneher Hi Richard, thanks for the very interesting analysis. I noticed on page 3 "The probability that offspring genomes are identical to their parents is u = 1 − e−μt", is it a typo? I thought the u should be just e−μt when there is zero mutation.

[Haogao Gu @GuHaogao]

Thanks @chasewnelson who developed SNPGenie which is very helpful in the selection pressure analysis!

[Haogao Gu @GuHaogao]

We investigated within-host evolution of SARS-CoV-2 using HK deep sequencing data from 2020 to 2022 in this study. Potential lineage-specific and vaccination-specific effects were discussed. https://t.co/PUamvKKqrR

[Leo Poon @world_epidemic]

Does vaccination affect intra-host SARS-CoV-2 diversity? Do different variants have different abilities to explore sequence space?

Here is our @HKU_SPH @GuHaogao @ahmedaquadeer PREPRINT to answer these questions:
https://t.co/f4UL4rN289

[Leo Poon @world_epidemic]

Glad to be involved in this excellent #Omicron study from Hui-Ling Yen @HKU_SPH.

Looks omicron variants behave differently from the ancestral #SARSCoV2 in hamsters.

https://t.co/mxXyzwqtWT

[Sophie Valk @svalko3]

Priming conditions for broadly neutralizing SARS antibodies- a great collaboration from HK @MalikP46697504 @nancyleung_hk, China and Singapore @linfa_wang @CheeWahTan2. A fav figure I could study all day by @GuHaogao @Janice22461665 https://t.co/ViF9z7o18l

[Leo Poon @world_epidemic]

Our BA.1/BA.2 is now published in EID.
⁦@GuHaogao⁩

Early Release - Recombinant BA.1/BA.2 SARS-CoV-2 Virus in Arriving Travelers, Hong Kong, February 2022 - Volume 28, Number 6—June 2022 - Emerging Infectious Diseases journal - CDC https://t.co/1pDTPb6Esr

[Máiréid @MaireidB]

So happy to see this work with @svalko3, @world_epidemic, and @GuHaogao from my PhD project at @hkumed published! We examined the effects of T cell pressure on the flu genome in the context of Next Gen vaccination 🧬 https://t.co/0Pp1PKgbMv

[Haogao Gu @GuHaogao]

We @world_epidemic identified a BA.1/BA.2 recombinant virus in incoming travellers in Hong Kong. The recombinant virus was confirmed by both repeated NGS sequencing and clone of RT-PCR product. We have just submitted it for Pango designation, see below:
https://t.co/hB301tknm6

[Leo Poon @world_epidemic]

We detected a recombinant between #Omicron subvariants BA.1 and BA.2. It was detected in early Feb from two epidemiologically linked cases. This recombinant has a breakpoint at around the 5' end of spike. We cannot find this viral genome in commonly used sequence database. /1