Discussion - Thoughts on a global outbreak of monkeypox

[kiwibird]

Data is for smallpox - but extrapolation seems fair.

[kiwibird]

6 days incubation for "direct innoculation" and 8 - 16 days for aerosol..... explains the delay in "non direct" contacts symptoms.... h/t @jmcrookston on twitter. https://twitter.com/jmcrookston/stat...86551753854977 Links to WHO data on monkeys in thread.

[alert]

I mean, well sure, the USSR worked on it. But they also worked on a lot of other nasty stuff, including weaponized forms of plague, smallpox, anthrax, etc. The source cited in this article hasn't been in Russia in almost 30 years.

[alert]

Russia was planning to use monkeypox as bioweapon, claims ex-Soviet scientist - World News (wionews.com)

[kiwibird]

They are also vaccinating sexual health care workers.

[JJackson]

The NCBI databank now has a complete sequence (MPXV_USA_2022_MA001 # ON563414) which is aligned with the sequences anticipated as being the problem branch in my original post in this thread ( see phylogenetic tree in post #5 ) note in particular MN648051 (Israel 2018) which is the closest match and I used for my alignment giving a 99.96% homology or about 80 SNPs over the full genome. This is rather more than the ~20 SNPs (estimated from branch length) indicated in the Virological.org partial Portuguese sequence Monkeypox/PT0001/2022.

Monkeypox3.JPG

My speculative working hypothesis at this point is that drift in the WA branch of the genome has allowed pre-symptomatic - or possibly asymptomatic - infection via the anal mucosa which has not come to light in West Africa where homosexuality is largely taboo. Introduction into more liberal areas has allowed spread and, if not contained, will allow further adaption. If this is correct then the vaginal mucosa is also likely to be a target. Endoscopic examination of the anal cavity would seem a logical step looking for lesions.

[sharon sanders]

Welcome Zeffy!

[Zeffy]

In possible relation to the case from Gran Canaria, there was a pride festival (Gay Pride Maspalomas) between 5/5/22 and 15/5/22 on Gran Canaria.

Although it is important not to place any stigma upon these cases, as cautioned by others, this may be relevant as it could possibly explain why so many same generation cases were found in people in different places, if these cases were attained at a shared holiday destination.
Notably, Canary Islands are a popular destination for Spanish, Portugese and British Travellers.
Hopefully Epi interviews would elucidate any shared transmission sites.

[Emily]

I'm glad this monkeypox virus looks like the SOS. Otherwise, this crazy tabletop exercise from last year might worry me.

https://www.nti.org/wp-content/uploa...-TTX_Final.pdf
Jaime M. Yassif, Ph.D.
Kevin P. O’Prey, Ph.D.
Christopher R. Isaac, M.Sc.
Strengthening Global Systems
to Prevent and Respond to
High-Consequence Biological Threats
Results from the 2021 Tabletop Exercise Conducted in
Partnership with the Munich Security Conference
SUMMARY
In March 2021, NTI partnered with the Munich Security Conference to
conduct a tabletop exercise on reducing high-consequence biological threats.
The exercise examined gaps in national and international biosecurity and
pandemic preparedness architectures—exploring opportunities to improve
prevention and response capabilities for high-consequence biological
events. This report summarizes the exercise scenario, key findings from
the discussion, and actionable recommendations for the international
community
....

Move 3(May 10, 2023) occurred 12 months after the initial outbreak, with more than 480 million cases and
27 million fatalities globally (Figure 4). At this stage, participants learn that the pandemic was caused by a
regional bio-terror attack that far exceeded the perpetrators’ goals.

Specifically, Brinian intelligence reveals that the engineered monkeypox virus was developed illicitly at
the fictional country of Arnica’s leading institute for virology. Arnica (population 75 million) has a history
of conflict with neighboring Brinia (see map in Figure 5). An independent Arnican terrorist group—the
SPA—had worked with sympathetic laboratory scientists to
engineer a highly contagious, deadly pathogen and disperse
it at crowded train stations in Brinia during the national
holiday, when much of the population was travelling
domestically and internationally.
The SPA had exploited the Arnican government’s weak
oversight of its bioscience research laboratories. SPA
sympathizers working in Arnica’s leading virology institute
used publicly available scientific publications to guide their
work to modify the monkeypox virus to make it more
transmissible and resistant to currently available vaccines.
The discussion in Move 3 focused on governance of dual-
use bioscience research as well as current weaknesses in
biosafety and biosecurity systems that exacerbate biological
risks...

[Emily]

I've been reading up on the history of monkeypox. Very strange, only found in lab monkeys for decades. In this case the pox lesions were seen after the animals were tattooed and only at that site. So maybe with some variants, breaking the skin opens the skin to the virus in the interior.
https://www.ncbi.nlm.nih.gov/pmc/art...00262-0121.pdf

[Emily]

Very interesting. Nordic is headquartered in the same city where the first monkeypox outbreak occurred in 1958 in lab monkeys.

"In a bizarre coincidence, Bavarian Nordic held a meeting with Heymann and nine other public health leaders from around the world this week, planned 6 months ago, to discuss the need for more countries to stockpile its vaccine, given the increase in monkeypox cases over the past few years. "

[Emily]

https://www.medpagetoday.com/special...clusives/98857
Draft Genome Sequence of Latest Monkeypox Virus Unveiled

— No indication latest strain is "substantially different" from those circulating in recent years

by Sophie Putka, Enterprise & Investigative Writer, MedPage Today May 20, 2022
The latest monkeypox virus now popping up in multiple countries appears most closely related to a strain that circulated in 2018-2019, according to a draft genome sequence of a recent case.

Sequencing of a skin lesion sample from an infected male patient in Portugal -- where at least 20 confirmed cases have been reported -- suggests the latest monkeypox virus belongs to the West African clade. It is most closely related to cases that spread from Nigeria to the U.K., Israel, and Singapore in 2018 and 2019, reported João Paulo Gomes, PhD, of the National Health Institute Doutor Ricardo Jorge in Lisbon, and colleagues.

The group, who published their findings on the preprint server virological.org, said the draft genome sequence "will certainly contribute to better understand the epidemiology, sources of infection, and transmission patterns."..

[Emily]

Alert is correct.
https://www.medpagetoday.com/special...clusives/98857
Also reporting West African clade here:
https://flutrackers.com/forum/forum/...onkeypox-cases

[Mary Wilson]

Report of Monkeypox cases in 2018 in the United Kingdom

Published on 14 Feb 2019

Author: Mohana Priya Kunasekaran

DOI: http://doi.org/10.31646/gbio.22

... The first case of monkeypox recorded in the UK and in the European Union (EU) was on 8 September 2018, in a Nigerian resident residing at a naval base in Cornwall, UK (1, 2). The patient was suspected to have been infected in Nigeria before travelling to the UK.

... From previous outbreaks, the CFR has been between 1-10% (18). Two genetic clades of monkeypox virus, the West African Clade and Congo Basic clade, have been defined in the literature. According to available data, the Congo basic clade in more common than the West African clade and is endemic to the DRC (19). The West African Clade is associated with milder disease and fewer deaths and has a CFR <1%, while the Congo Basin clade has CFR up to 11% and previously documented human-human transmission (20).

In September-December 2017, the West African clade was identified in the Nigerian outbreak and, based on NCDC data, had a CFR of 2.9% with 68 confirmed cases from 197 suspected cases across 22 states (14). In 2018, based on NCDC data, the CFR was 2.2% with 45 confirmed cases from 114 suspected cases across 13 states. The same West African clade was reported (15).

https://jglobalbiosecurity.com/artic...31646/gbio.22/

[Mary Wilson]

First monkeypox genome from latest outbreak shows links to 2018 strain

20 May 2022
Michael LePage

The first draft genome of the virus responsible for the rapidly growing monkeypox outbreak has been released online by a team in Portugal. The DNA sequence shows it is of the mild West African type and most closely related to the monkeypox viruses detected in the UK, Singapore and Israel in 2018 and 2019.

What isn’t yet clear is whether this virus has any changes that make it more transmissible in humans, which would explain why the current outbreak is so widespread and by far the largest seen outside Central and West Africa, where the virus spreads in monkeys. This could take some time to establish, given that monkeypox has a large and complex genome.

At the time of writing, there were 127 confirmed and suspected cases of monkeypox in 10 countries, including the US, UK and Australia, and researchers suspect the true numbers are even higher.

João Paulo Gomes and colleagues at the National Institute of Health in Portugal sequenced a sample taken from a male patient on 4 May. Teams in other countries are also sequencing viral samples from the outbreak, but Gomes’s team is the first to make a sequence public.

Gustavo Palacios at Icahn School of Medicine at Mount Sinai, New York, says the draft sequence from Portugal has too many gaps to draw firm conclusions, but that he has seen a more complete sequence from a team in Belgium. “As far as I can see, it seems to be identical to the one in the UK in 2018,” says Palacios. “That is a little bit odd.”

In 2018, there were three cases in the UK after someone returning from Nigeria infected two other members of their household.

As more samples are sequenced, it should become clear whether, as suspected, a single variant of monkeypox is responsible for all the cases in the latest outbreak.

https://www.newscientist.com/article...o-2018-strain/