Rapid Expansion Beyond the Amazon Basin: Oropouche Virus joins other main arboviruses in epidemic activity across the Americas - A comprehensive genomics of new pathogen in real-time - A thread & open access scientific report 🔽 @Mittenavoig @fiocruz_enclimade.health/2024/08/04/rap… Oropouche virus, detected in Trinidad and Tobago in 1955, has been confined to the Amazon Basin. But since late 2022,spread to northern Brazil to urban centers in Bolivia, Colombia, Cuba, and Peru.

The number of Mpox cases double in South Africa. In total, 13 cases were detected and two deaths reported. In a short thread, I explain what we know about the Mpox outbreak in SA and what the country is doing to respond. 🧵 Yesterday, the National Department of Health reported another 6 cases of Mpox in South Africa, basically doubling the number of known cases on the largest outbreak ever recorded in SA. news24.com/news24/southaf…

A summary of Mpox outbreaks, new variants & deaths in South Africa and Africa that we are tracking and make data public in real time. Clade IIb causing first 2 deaths in SA and new variant, Clade Ib, emerging in mining town in DRC. A short thread ⬇️ This week, the minister of health of SA released the news of an outbreak in the country. When he released the news on Wednesday, there was 5 cases and 1 death. By Saturday, there was 7 cases and 2 deaths.

In South Africa, today, the Health Minister reported the first death due to Mpox. In addition, 5 cases are now confirmed since 8 May 2024. Suggesting that SA is experience its first large outbreak of Mpox. A summary thread on what we know on the Mpox situation in SA⬇️ Investigation of the cases, by the NICD suggest local transmission as none of the 5 cases had an history of travel outside SA. In addition, the cases were unlinked cases found in two provinces in Gauteng and KwaZulu-Natal (the two largest provinces in SA).

Africa’s cholera crisis worsens amid extreme weather events. “The outbreaks are getting much larger because the extreme climate events are getting much more common,” Tulio de Oliveira - A photojournalism piece covering extreme events & the worst cholera in Africa @AlJazeera @AP Hospital beds in a ward dedicated to cholera patients at a government hospital in Lusaka. [Tsvangirayi Mukwazhi/AP Photo]Southern Africa’s latest outbreaks can be traced to the cyclones and floods that hit Malawi in late 2021 and early 2022, carrying the cholera bacteria to areas it does not normally reach.

Release of 8 new genomes of a new lineage of SARS-CoV-2 with > 100 mutations from South Africa. This is probably the most divergence lineage identified this year. In this thread, we highlight some of the characteristics of the new BA.2.X lineage and epidemiology in SA. So far, this has been detected from eight samples from three districts in Limpopo and Gauteng provinces (Capricorn, City of Johannesburg and City of Tshwane) between 20 September and 29 November 2023. All eight genomes were sequenced by the NICD from SARS-CoV-2 genomic surveillance (routine diagnostic samples) or syndromic GP-based surveillance (Viral Watch) @nicd_sa

South Africa has today detected a 3rd case of BA.2.86. In total, 3 genomes, 2 from Gauteng & 1 from Mapumalanga. Since the discovery of the first case, scientists advising the government have been alerted, here, I summarise SA advisory to this new lineage of COVID-19 🧵 South Africa is one of few countries of the world that still have an active genomics surveillance program and a scientific advisory board for the COVID-19 pandemic, which is called the Ministerial Advisory Board (MAC) that advise the ministers.

A small thread on COVID recombinants:
- Omicron XBB.1.5 in U.S.A. with key Spike F486P mutation
- Omicron/Delta XAY in SA also with F486P.

The XBB.1.5 seems to be fast increasing prevalence, whereas XAY faded. Will XBB.1.5 spread further? What is the role of the F486P mutation? A new recombinant lineage of Omicron XBB.1.5 seems to be emerging in the U.S.A. Very early data puts to an evolution of XBB.1.5 lineage to get a 'key mutation' F486P (Purple collar on graph, high prevalence in the East Coast).

A small thread on:
1) Why we are alerted but not too concerned of the global effects of the massive wave of COVID-19 in China,
2) Why the proposed restrictions from Italy & USA are not likely to be effective.
3) Some simple global interventions for 2023. China decided to stop its Zero-COVID intervention. The intervention worked well in the past two years and allowed time for the world and China to develop vaccines, diagnostics and therapeutics. Now, there is fear that the COVID-19 tsunami in China will detail the global efforts.

Like many scientists, I am also not convinced that Omicron evolved stepwise in Africa and was undetected for months. In the next tweets, I highlight some of my thoughts on this report and highlight some of the weaknesses. 1/x

https://twitter.com/ScienceMagazine/status/1598414246416629761

First, the 'fishing' of intermediates in Africa should also have been performed in Europe and the USA, which were the regions of the world that introduced the majority of Omicron lineages to Africa - medrxiv.org/content/10.110…

Update of COVID-19 variants in South Africa. A new Omicron lineage (BQ.1/BQ.1.1) has been recently detected in South Africa. It is still at small prevalence (5-10%). Infectious numbers are low as well positivity rate, number of hospitalisation and deaths. A small thread 1/x The Network for Genomics Surveillance in South Africa (NGS-SA) is alerted and has increased genomics surveillance. Our last genomes are less than 1 week old and show some increase of BQ.1 & BQ.1.1. We are current not concerned due to high population immunity and low infections.

In order to develop our shared vision of Global Science that values, respect & build on expertise in the Global South, we embark in an exciting & collaborative journey around the world & bring many scientific activities to Africa. This week, starts the 1st #NobelAfrica symposia The #NobelAfrica Symposia provide a unique opportunity to support and showcase advanced research and scholarship on the African continent, and to promote research excellence and collaborative scholarship in Africa in conversation with the rest of the world.

The African Scientific Dream Team strikes again! Today a scientific report in Science, revealed that a large consortium of over 300 African scientists and public health institutions illustrated how the SARS-CoV-2 variants reached and spread across Africa. science.org/doi/10.1126/sc… The study shows that most of the introductions of variants in Africa were from abroad and not from Africa. The consortium found that the initial waves of infections in Africa were primarily seeded by multiple introductions of viral lineages from abroad (mainly Europe).

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.

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.

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.

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.

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

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!

Fine et al. 1998 pubmed.ncbi.nlm.nih.gov/2850277/ 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/

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

Summary of BA.4 & BA.5 in South Africa
- 100% of infections
- Fuelling 5th wave
- Low testing & high positivity ratio
- Increasing number of hospitalizations, however still much lower than in previous waves
- SA may guide the world on the future of the pandemic South Africa had multiple waves of infections, the first dominated by multiple lineages (> 50 614G lineages), the second by Beta, them Delta, Omicron BA.1, BA.2 and Omicron BA.4 and BA.5.