1. The characterization and clinical manifestation of the SARS-CoV-2 outbreak in Uruguay
 
Collaborating Parties:
Victoria Elizondo, Victoria Perez -Natalia Mazza Carolina Beloso, Silvana Ifran, Mariana
Fernandez, Andrea Santini, Veronica Perez, Veronica Estevez, Matilde Nin, Gonzalo Manrique,
Leticia Perez, Fabiana Ross, Susana Boschi, Maria Noel Zubillaga, Raquel Ballestea – Laboratorio
de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay.
Batsirai Mabvakure – Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD,
USA.
Paul Zappiled Christian Marier- Genome Technology Center, Office for Science and Research,
NYU Langone Health, New York, NY, USA .
Victoria Perez- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de
Medicina, Udelar, Montevideo, Uruguay.
Carolina Beloso- Departamento de Biodiversidad y Genética. Instituto de Investigaciones
Biológicas
Clemente Estable, Montevideo, Uruguay.
Matthew T. Maurano – Institute for Systems Genetics, NYU Grossman School of Medicine, New
York, NY, USA.
Simon Dellicour- Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, Bruxelles,
Belgium; Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven,
Belgium.
Adriana Heguy, Ralf Duerr – Department of Pathology, NYU Grossman School of Medicine, New
York, NY, USA.

Nature and purpose:
To identify SARS-CoV-2 introductions into Uruguay and their subsequent transmission dynamics
to better understand disease patterns and regional aspects of the pandemic in Latin America

Output in the last 12 months:
One paper was submitted in 2020 (and published in January 2021)

Future Direction:
This is an ongoing collaboration that is now focused on generating the genomic sequence data
from the second wave of the pandemic in Uruguay. Our priority will be detection of the presence of
potential vaccine escape variants and other potentially problematic variants of concern.

2. The evolutionary dynamics of SARS-CoV-2 lineages during the first epidemic wave in
New York City.
 
Collaborating Parties:
Simon Dellicour- Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, Bruxelles,
Belgium.
Bram Vrancken, Samuel L. Hong, Guy Beale – Department of Microbiology, Immunology and
Transplantation, Rega Institute, Leuven, Belgium.
Matthew T.Maurano – Institute for Systems Genetics, NYU Grossman School of Medicine, New
York, NY, USA.
Antoine Chaillon – Division of Infectious Diseases and Global Public Health, University of California
San Diego, CA, USA.
Sitharam Ramaswami, Paul Zappile, Christian Marier – Genome Technology Center, Office for
Science and Research, NYU Langone Health, New York, NY, USA
Adriana Heguy, Ralf Duerr – Department of Pathology, NYU Grossman School of Medicine, New
York, NY, USA.

Nature and purpose:
Phylogeographic investigation to elucidate the circulation of viral lineages during the first months of
the New York outbreak – the epicentre of the COVID-19 epidemic in the United States.

Output in the last 12 months:
One paper was published in PLoS Pathogens in 2021. 

Future Direction:
This is an ongoing collaboration that will shift its focus to the COVID-19 pandemic in other areas in
the USA and beyond

3. Investigating the role of natural selection in the emergence and ongoing evolution of the
N501Y lineages (V1-V3) of SARS-CoV2.
 
Collaborating Parties:
Darren P Martin – Institute of Infectious Diseases and Molecular Medicine, Division Of
Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town,
South Africa.
Steven Weaver, Stephen D Shank, Sergei L Kosakovsky Pond – Institute for Genomics and
Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA.
Houryiah Tegally, Emmanuel James San, Eduan Wilkinson, Jennifer Giandhari, Sureshnee
Naidoo, Yeshnee Pillay, Lavanya Singh, Richard J Lessells, Tulio De Oliveira – KwaZulu-Natal
Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical
Sciences, University of KwaZulu- Natal, Durban, South Africa NGS-SA –
(http://www.krisp.org.za/ngs-sa/ngs-sa_network_for_genomic_surveillance_south_africa/).
COVID-19 Genomics UK (COG-UK) – (https://www.cogconsortium.uk).
Ravindra K Gupta – Clinical Microbiology, University of Cambridge, Cambridge, UK;
Africa Health Research Institute, KwaZulu-Natal, South Africa.
Joel O Wertheim – Department of Medicine, University of California San Diego, La Jolla, CA 92093,
USA.
Anton Nekturenko – Department of Biochemistry and Molecular Biology, The Pennsylvania State
University, Pennsylvania, USA.
Ben Murrell – Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet,
Stockholm, Sweden.
Philippe Lemey – Department of Microbiology, Immunology and Transplantation, Rega Institute, KU
Leuven, Leuven, Belgium.
Oscar A MacLean, David L Robertson – MRC-University of Glasgow Centre for Virus Research,
Scotland, UK.

Nature and purpose:
To examine temporal patterns of natural selection within protein coding sequences of the N501Y
viral lineages since the emergence of SARS-CoV-2 in 2019.

Output in the last 12 months:
One paper was published in  the journal Cell in 2021 .

Future Direction:
Surveillance of the rapidly growing pool of SARS-CoV-2 genomic sequence data for the presence
of potential vaccine escape variants and other potentially problematic variants of concern in South
Africa and beyond will be continued.

4. Selection Analysis Identifies Unusual Clustered Mutational Changes in Omicron Lineage
BA.1 that Likely Impact Spike Function.

Collaborating Parties:
Darren P Martin, Arne De Klerk – Institute of Infectious Diseases and Molecular Medicine, Division
Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape
Town, South Africa.
Philippe Lemey – Department of Microbiology, Immunology and Transplantation, Rega Institute, KU
Leuven, Leuven, Belgium.
Steven Weaver, Stephen D Shank, Sergei L Kosakovsky Pond – Institute for Genomics and
Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
Houryiah Tegally, Emmanuel James San, Eduan Wilkinson, Jennifer Giandhari, Richard J
Lessells, Anton Nekrutenko, Tulio De Oliveira – KwaZulu-Natal Research Innovation and
Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of
KwaZulu- Natal, Durban, South Africa NGS-SA.
Ben Murrell – Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet,
Stockholm, Sweden.
Carolyn Williamson – Division of Medical Virology, Institute of Infectious Disease and Molecular
Medicine, University of Cape Town, Cape Town, South Africa.
Spyro Lytras, Oscar S MacLean, David L Robertson, Richard J Orton – MRC-University of Glasgow
Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
Alexander G Lucaci – Institute for Genomics and Evolutionary Medicine, Department of Biology,
Temple University, Philadelphia, PA 19122, USA.
Wolfgang Maier, Bjorn Gruning – Bioinformatics Group, Department of Computer Science,
University of Freiburg, Freiburg, Germany.
Maciej F Boni – Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania
State University, University Park, PA, USA.
Cathrine Scheepers, Jinal N Bhiman – National Institute for Communicable Diseases (NICD) of the
National Health Laboratory Service, (NHLS), Johannesburg, South Africa, SA MRC Antibody
Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the
Witwatersrand, Johannesburg, South Africa.
Josie Everatt, Daniel G Amoako – National Institute for Communicable Diseases (NICD) of the
National Health Laboratory Service, (NHLS), Johannesburg, South Africa.
James Emanuel San, Jennifer Giandhari – KwaZulu-Natal Research Innovation and Sequencing
Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-
Natal, Durban, South Africa.
Alex Sigal, Ravindra K Gupta – Africa Health Research Institute, Durban, South Africa.
Nei-yuan Hsiao – Division of Medical Virology, University of Cape Town and National Health
Laboratory Service, Cape Town South Africa.
Anne von Gottberg – National Institute for Communicable Diseases (NICD) of the National Health
Laboratory Service, (NHLS), Johannesburg, South Africa
Robert W Shafer – Division of Infectious Diseases, Department of medicine, Stanford university,
Stanford, CA, USA
Robert J Wilkinson – Wellcome Center for Infectious Diseases Research in Africa, Institute of
Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town,
South Africa
Brian Trevor Sewell – Structural Biology Research Unit, Department of Integrative Biomedical
Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town,
South Africa
Allison J Greaney, Tyler N Starr, Jesse D Bloom – Basic Sciences Division and Computational
Biology Program, Fred Hutchinson Cancer Research Center, Seattle; Department of Genome
Sciences & Medical Scientist Training Program, University of Washington, Seattle, Howard
Hughes Medical Institute, Seattle, WA

Nature and purpose:
To determine what drives the mutational changes in the Omicron variant of concern (VOC).

Output in the last 12 months:
One paper published in 2022 in the Journal Molecular Biology and Evolution.

Future Direction:
This is an ongoing collaboration.

5.Conserved recombination in coronavirus subgenera 
Collaborating Parties:

Darren P Martin, Arné de Klerk, Phillip Swanepoel, Mpumelelo Zondo, Isaac Abodunran – Institute
of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of
Integrative Biomedical Sciences, University of Cape Town
Rentia Lourens – Division of Neurosurgery, Neuroscience Institute, Department of Surgery,
University of Cape Town
Spyros Lytras, Oscar A MacLean, David Robertson – MRC-University of Glasgow Centre for Virus
Research, University of Glasgow, Glasgow
Sergei L Kosakovsky Pond, Jordan D Zehr – Institute for Genomics and Evolutionary Medicine,
Department of Biology, Temple University, Philadelphia
Venkatesh Kumar, Ben Murrell – Department of Microbiology, Tumor and Cell Biology, Karolinska
Institutet, Stockholm, Sweden
Michael J. Stanhope – Department of Population and Ecosystem Health, College of Veterinary
Medicine, Cornell University, Ithaca, NY

Nature and purpose:
To determine whether recombination is non-random in coronavirus subgenera.

Output in the last 12 months:
One article has been accepted in the journal Virus Evolution.

Future Direction:
This is an ongoing collaboration.

6. T cell immune escape mutations at HLA-binding anchor motifs found in SARS-CoV-2
epitopes from genomes isolated in South Africa and subSaharan Africa

Collaborating Parties:
Nobubelo Ngandu – SAMRC
Burtram Fielding – University of the Western Cape
Wendy Burgers – University of Cape Town
Zabrina Brumme – Simon Fraser University, Canada
Nature and purpose: 
Prediction and monitoring of T cell immune escape mutations at HLA-binding anchor motifs found
in SARS-CoV-2. 

Output in the last 12 months:
None.

Future Direction:
This is an ongoing collaboration funded by SAMRC for 2022.

7. HIV-1 Latent Viral Reservoir Dynamics
 
Collaborating Parties:

Melissa-Rose Abrahams, Lynn Tyers, David Matten, Deelan Doolabh, Colin Anthony, Carolyn
Williamson – Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine,
University of Cape Town
Salim Abdool Karim – Centre for the AIDS Programme of Research in South Africa, University of
KwaZulu- Natal
Andrew Redd – Johns Hopkins University, School of Medicine in Baltimore, USA.
Siposethu Matzishana, Nkosazama Nyembezi – SANBI

Nature and purpose:
To study the viral dynamics involved in HIV-1 subtype C latent reservoir formation maintenance
and evolution to better understand the determinants thereof.

Output in the last 12 months:
None.

Future Direction:
This project is funded by the National Institutes of Health (NIH) USA and the South African Medical
Research Council and will run between 2020 and 2025.
 
8. Phytovirus Diversity

Collaborating Parties:
Philippe Roumagnac, Denis Filloux, Charlotte Julian and Emmanuel Fernandez – CIRAD,
Montpelier, France.
Pierre Lefeuvre, Frederic Chiroleux and Jean-Michel Lett – CIRAD, UMR PVBMT, Réunion Island,
France.
Thierry Candresse, Armelle Marais, Marie Lefebvre and Chantal Faure – INRA, UMR BFP,
Villenave d’Ornon France.
Darren Martin – UCT, South Africa.
Arvind Varsani – Arizona State University, USA.
Pascal Gentit and Benoir Remenant – ANSES France.
Francois Mesleard and Hugo Fontes – La Tour du Valat, France.
Christophe Levergne – CBN CPIE Mascarin.
Anne Duputie and Francois Massol – UMR Evo-Eco-Paleo, France.

Nature and purpose:
While it is well established that emerging viruses generally originate in uncultivated hosts with
which they have well-established interactions, we currently know almost nothing about the diversity
and the distribution of phytoviruses circulating in either natural or managed ecosystems. This
project proposes (i) to develop an integrated approach to reveal the phytoviral species richness of
plant communities within several unmanaged and managed ecosystems, (ii) to experimentally
study the effect of controlled plant communities on phytovirus species richness, and (iii) to search
phytovirus nucleotide sequence data in silico evidence of the evolutionary footprints adaptation to
a new host species.

Output in the last 12 months:
Plant samples were first collected in South Africa in 2019 but the field sampling trips planned for
2020 and 2021 was postponed until October 2022 and scheduled annually thereafter until 2025,
pandemic conditions permitting. Efforts to detect phytoviruses in our plant samples are currently
being performed in the laboratory of Philippe Roumagnac in Montpellier France.

Future Direction:
This is an ongoing project that is funded until 2023.