Most important sentences of our most recent peer-reviewed publication :
Every case of monkeypox infection should be treated with the same attention and sense of urgency as the ones now in European countries and North America.
The entire epidemic of hMPXV regardless of the location needs to be halted, not just this Northern hemisphere outbreak.
We hope that the world provides the funding and focus for effective regional and global public health surveillance for emerging and re-emerging threats.
By supporting a non-discriminatory and non-stigmatizing classification, we can encourage African and other researchers in low- and middle-income countries (LMICs) to advance genomic surveillance, share sequence data, and minimize negative impacts.
Failure to support and adopt the proposed nomenclature and classification may result in loss of interest in sustaining active surveillance and rapid reporting of pathogens with epidemic and pandemic potentials by scientists and institutions in Africa and other LMICs.
Manuscript published after peer review #PLOSBiology & agreement with @WHO -
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus dx.plos.org/10.1371/journa…
Need to thank to the brave international scientists, medical personnel & public health officials that work day and night to control epidemics and understand that stigma and discrimination fuel epidemics. Thanks @christian_happi@trvrb@GISAID@firefoxx66@houzhou@IfedayoTiffy
I will just
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Omicron BA.5 went to dominate most of the recent COVID infections in the world. This lineage was first identified in April 2022 in South Africa. The paper that describes the emergence of the BA.4 & BA.5 is now final and OPEN at Nature Medicine - nature.com/articles/s4159…
As the previous Omicron lineages BA.1, BA.2, BA.3, the BA.4 and BA.5 was identified close to the largest airport and main economic hub of South Africa, in Gauteng. Interesting, BA.5 went a large application event in Durban, the capital of KwaZulu-Natal and SA biggest harbour.
KwaZulu-Natal, home of Durban, was the province that BA.5 (in orange) went to dominate infections quicker. It is still not clear why BA.5 has an advantage over BA.4 as they have identical Spike proteins.
Thread for our latest publication on the intrahost evolution of SARS-CoV-2 virus in an immunocompromised individual with HIV in South Africa for at least 270 days with consistently replicating viruses at a high viral load. 1/n academic.oup.com/cid/advance-ar…
The patient was a 22-year-old female with uncontrolled advanced HIV infection who was persistently infected with the SARS-CoV-2 Beta variant for 9 months. Phylogenetic analysis confirmed the infecting virus from three swabs clustered together on a background of 7977 sequences.
> 270 days, the virus acquired at least 10 mutations in the spike glycoprotein and 11 mutations outside spike. The additional spike mutations included six in RBD (S371F, N450D, A475V, F490Y, S494P and Q498R); a deletion at 141-143 NTD which leads to neutralizing antibody escape.
Finally out after peer-review @NatureMedicine:
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. In this publication, we describe the origins, evolution and impact of BA.4 & BA.5, which emerged in SA and now dominate most of the global COVID infections. 1/x
BA.4 & BA.5 emerged between Johannesburg & Tshwane. This region is in close proximity to the largest airport in Africa. The lineages could come from anywhere and quickly spread in SA. BA.5 went through amplification in Durban. BA.5 is starting to dominate most global infections.
There is much recent discussion on the origin of BA.4 and BA.5. Bayesian phylogenetic methods revealed that BA.4 and BA.5 are distinct from the other Omicron lineages (Molecular clock signal: correlation coefficient = 0.6, R2 = 0.4).
We propose a novel non-discriminatory & non-stigmatizing classification of monkeypox aligned with best practices in the naming infectious diseases to minimize negative impacts on nations, economies & people and consider the evolution & spread of the virus virological.org/t/urgent-need-…
Why we did do this? In the current classification of monkeypox genetic diversity, only two clades are recognized – referred to as West African & the Central African or Congo Basin clades. However, these historic names are counter to the best practices and generate discrimination
In the context of the current global outbreak, continued reference to this virus being African is not only inaccurate but also discriminatory & stigmatizing. The most obvious manifestation is the use of photos of African patients to depict the pox lesions.
As scientists working in infectious diseases, the first thing that we do when a virus reemerges is to read the scientific literature. Ten MonkeyPox scientific publications that I read yesterday, thanks @rjlessells for the list!
Genomic variability of monkeypox virus among humans, Democratic Republic of the Congo. Kugelman et al. Emerg Infect Dis. 2014 - pubmed.ncbi.nlm.nih.gov/24457084/
Multistate outbreak of monkeypox--Illinois, Indiana, Kansas, Missouri, Ohio, and Wisconsin, 2003. MMWR Morb Mortal Wkly Rep. 2003 - pubmed.ncbi.nlm.nih.gov/12855947/
BA.4 & BA.5 Recent Developments:
- Wave of infections in SA has peaked with, so far, low hospitalizations & deaths
- Rapid increase of infections in Portugal, with older & highly vaccinated population
- Resurgence in both countries without BA.2 wave
- ECDC listed as VOCs
In the last weeks, we exchanged information with Portuguese colleagues, specially @borges__vitor who is doing a great job at Genomics Surveillance. Here, comparisons between South Africa & Portugal may help the world to understand more about the early spread of BA.4 & BA.5
Both South Africa and Portugal had a large Omicron BA.1 wave, which finished around 3 months ago. The BA.1 wave was followed by BA.2 but did NOT cause a large increase in infections. Graphic by @houzhou and data by @borges__vitor@GISAID