National Institute for Communicable Diseases (NICD) - Comprehensive Analysis Report

Summary

The National Institute for Communicable Diseases (NICD) is South Africa's national public health institute, operating as a vital division of the National Health Laboratory Service (NHLS). Its mission is to be a leading source of knowledge and expertise in regionally relevant communicable diseases for the South African Government, Southern African Development Community (SADC) countries, and the broader African continent. The NICD assists in policy and program planning and supports responses to communicable disease threats. Its vision is to effectively respond to communicable disease threats as a national public health institute for South Africa. The institute plays a critical role in public health by issuing warnings on outbreaks, providing weekly surveillance reports, and identifying and characterizing infectious agents.

1. Strategic Focus & Objectives

Core Objectives

The NICD's core objectives revolve around a multi-faceted approach to communicable disease control and prevention:

Disease Surveillance and Outbreak Response: This is a primary function, supported by an Outbreak Response Unit (ORU) and an Emergency Operations Centre (EOC), focusing on detecting and responding to outbreaks and epidemics.

Specialised Diagnostic Services: The institute functions as a reference laboratory, offering extensive specialised diagnostic services for a wide range of communicable diseases.

Public Health Research: Engaging in directed and relevant research is crucial to understanding and managing national and regional public health problems associated with communicable diseases.

Capacity Building: The NICD is dedicated to strengthening capacity for communicable disease response nationally and regionally through various training initiatives, including the South African Field Epidemiology Training Programme (SAFETP) at Frontline, Intermediate, and Advanced tiers.

Policy and Programme Support: It provides technical support and expertise to the National Department of Health (NDoH) and other stakeholders for planning policies and programs aimed at communicable disease control and elimination.

Specialization Areas

The NICD is structured into various key centers, each specializing in specific areas:

Centre for Emerging Zoonotic and Parasitic Diseases (CEZPD)

Centre for Enteric Diseases (CED)

Centre for Healthcare-Associated Infections, Antimicrobial Resistance, and Mycoses (CHARM)

Centre for HIV and STIs (CHIVSTI)

Centre for Respiratory Diseases and Meningitis (CRDM)

Centre for Tuberculosis (CTB)

Centre for Vaccines and Immunology (CVI)

Public Health Surveillance and Response Division (DPHSR)

National Cancer Registry (NCR)

Target Markets

The NICD targets conditions prevalent in South Africa, the SADC region, and the African continent. This includes diseases such as HIV, tuberculosis, malaria, influenza, poliomyelitis, measles, arboviral infections, rabies, and viral haemorrhagic fevers.

2. Financial Overview

Funding History

The primary activities of the NICD are funded by the National Treasury of South Africa as a division of the National Health Laboratory Service. Specific research endeavors are often supported by external agencies, partners, and donors through direct funding or technical support.

Notable funding includes:

A cooperative agreement from the U.S. Centers for Disease Control and Prevention (CDC) for approximately $5,000,000 for Year 1 (Federal Fiscal Year 2022 funds), with annual award amounts for years 2-5 set at continuation. This funding is dedicated to providing accurate, timely, and high-quality strategic information to enable the South African Government to track critical infectious disease pathogens, monitor interventions, and inform policy. The period of performance is from September 30, 2022, through September 29, 2027.

Support from the Water Research Commission (WRC) and the Bill and Melinda Gates Foundation (BMGF) for the SARS-CoV-2 wastewater surveillance project.

Research funding from the National Institutes of Health's Vaccine Research Center and the South African Department of Science and Technology for HIV research.

Additional funders include the Wellcome Trust, Fogarty International Center, National Research Foundation, and the Poliomyelitis Research Foundation.

In the 2022/23 financial year, 27% of NICD's 513 employees were grant-funded or fixed-term personnel, highlighting a reliance on external, project-specific funding for certain operations.

3. Product Pipeline

Key Products/Services

The NICD is deeply engaged in various ongoing surveillance and research initiatives considered critical public health services:

GERMS-SA Programme: This national, population-based laboratory surveillance program, established in 2003, monitors bacterial and fungal infections. It provides strategic information on public health pathogens, including vaccine-preventable, epidemic-prone, healthcare-associated bloodstream infections with antibiotic resistance, HIV-associated opportunistic infections, and neglected tropical diseases. In 2023, GERMS-SA detected 14,138 surveillance cases.

Poliovirus Surveillance: The NICD supports sub-Saharan African countries in acute flaccid paralysis (AFP) and poliovirus detection surveillance. In 2022/23, 5,536 samples were processed, detecting wild poliovirus type 1 (imported from Mozambique) in seven cases and vaccine-derived poliovirus in multiple cases. Environmental surveillance identified Sabin/Sabin-like viruses and vaccine-derived polioviruses.

Measles Surveillance: The Centre for Vaccines and Immunology (CVI) tested 6,664 serum samples in 2022/23, with 995 (15%) confirmed positive for measles. This surveillance contributes to understanding disease patterns and informing public health interventions.

Mpox Reference Testing: The Centre for Emerging Zoonotic and Parasitic Diseases (CEZPD) provides reference laboratory testing for mpox in South Africa and other African countries. Genomic sequencing plays a key role in linking local cases to multi-country outbreaks.

Rabies Surveillance: The CEZPD performed 91 tests for suspected rabies cases between April 1, 2023, and March 31, 2024, contributing to control and prevention efforts.

COVID-19 Environmental Surveillance (SACCESS network): NICD led wastewater surveillance for SARS-CoV-2, analyzing 413 wastewater samples in 2022/23, identifying SARS-CoV-2 in 95% of samples and detecting viral variants using next-generation sequencing.

HIV Surveillance: Prof. Adrian Puren focuses on developing HIV surveillance programs, particularly for HIV incidence, utilizing "big data" to inform surveillance, monitoring, and evaluation.

Intussusception Surveillance: Active surveillance for intussusception cases, a rare intestinal blockage associated with rotavirus vaccines, is ongoing in seven South African cities.

Tuberculosis Surveillance: The Centre for Tuberculosis (CTB) conducts research to enhance microbiological and epidemiological surveillance of drug-resistant tuberculosis in South Africa, including assessing Whole Genome Sequencing (WGS) as a phylogenetic investigation tool.

Cancer Surveillance: The National Cancer Registry (NCR) oversees cancer surveillance and research, aiming to strengthen these areas in South Africa and the sub-Saharan African region, and explore the role of infections in cancer development in African populations. Dr. Mazvita Muchengeti leads the South African HIV Cancer Match Study.

4. Technology & Innovation

Technology Stack

The NICD leverages advanced technological platforms and scientific methodologies in its operations:

Biosafety Level (BSL) Laboratories: The institute operates Biosafety Level 3 (BSL-3) laboratories and is home to Africa's only suited high-containment BSL-4 laboratory. These facilities are essential for the safe handling of highly dangerous pathogens such as Ebola and Marburg viruses, positioning NICD as a premier research, surveillance, and diagnostics institution.

Sequencing Core Facility (SCF): The SCF conducts next-generation sequencing for diagnosis and outbreak support, playing a critical role in molecular epidemiology to investigate the source of outbreaks. This technology was crucial in detecting viral variants of SARS-CoV-2 and linking mpox cases to multi-country outbreaks.

Advanced Diagnostic Methods: The Centre for Enteric Diseases has evaluated rapid diagnostic methods like Taqman® Array Cards (TACs), capable of simultaneously detecting 19 different enteric pathogens and performing molecular serotyping of Salmonella enterica serovars.

Wastewater-Based Epidemiology: Through the SACCESS network, the NICD employs wastewater-based epidemiology for SARS-CoV-2 surveillance, enabling continuous monitoring of viral strains and informing public health measures.

Big Data Analytics: In HIV surveillance, the institute utilizes "big data" analytics to inform surveillance, monitoring, and evaluation strategies.

Mosquito Infection Studies: In collaboration with the Wits Research Institute for Malaria, the CEZPD conducts unique mosquito infection studies with Plasmodium malaria parasites, serving as a resource for novel host-parasite interaction studies and malaria transmission-blocking technologies.

5. Leadership & Management

Executive Team

The NICD is led by a multidisciplinary team of experts committed to public health demands.

Prof. Adrian Puren, Executive Director: Appointed in January 2022, Prof. Puren previously served as Deputy Director and Head of Virology (1999) and Head of the Centre for HIV and STIs (2017). His expertise lies in developing and implementing viral diagnostic platforms for EPI surveillance and diagnostic support, with a specific focus on HIV surveillance, incidence, and "big data" utilization. He also heads regional and national endpoint diagnostics laboratories for HVTN-supported vaccine and antibody-mediated prevention trials and is the quality assurance technical manager for the NICD.

Dr. Susan Nzenze, Acting Executive Deputy Director and Centre Head of the Division of Public Health, Surveillance and Response (DPHSR): A public health expert with nearly 15 years of experience, Dr. Nzenze has conducted surveillance studies on Pneumococcal Conjugate and Rotavirus vaccines, TB/HIV, and the Child Health and Mortality Prevention (CHAMPS) pilot. She holds an MPH (Health Economics) and a PhD in Public Health from the University of the Witwatersrand and is an Associate Professor at the University of Zimbabwe. She has over 35 peer-reviewed publications, secured Poliomyelitis Research Foundation (PRF) funding for three consecutive years, and is a trainer in the Data2Policy initiative. Her research interests include communicable and non-communicable disease surveillance and prevention, digital tools in healthcare, data-driven decision-making, and cost-effective public health interventions.

Centre Heads:

Dr. Jacqueline Weyer, Head of Centre: Centre for Emerging Zoonotic and Parasitic Diseases (CEZPD): A Principal Medical Scientist leading investigations into human rabies, viral hemorrhagic fevers, and other emerging zoonotic diseases. She holds a PhD in Microbiology and a Master of Public Health cum laude.

Prof. Cheryl Cohen, Centre for Respiratory Diseases and Meningitis (CRDM): Oversees the Centre for Respiratory Diseases and Meningitis.

Dr. Nishi Prabdial-Sing, Head of Centre: Centre for Vaccines and Immunology (CVI): Holds a PhD in Medical Virology. She supervises students, facilitates the virology program, coordinates medical science internship programs, and is a C2 NRF-rated researcher.

Dr. Shaheed Vally Omar, Centre for Tuberculosis (CTB): Leads the Centre for Tuberculosis.

Prof. Vindana Chibabhai, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM): Heads the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses.

Prof. Nicola Page, Centre for Enteric Diseases (CED): Leads the Centre for Enteric Diseases.

Dr. Mazvita Muchengeti, Centre Head: National Cancer Registry (NCR): A cancer epidemiologist overseeing cancer surveillance and research, focusing on strengthening these areas in South Africa and Sub-Saharan Africa. She leads the South African HIV Cancer Match Study.

Recent Leadership Changes

Prof. Adrian Puren was appointed Executive Director of the NICD in January 2022. Dr. Susan Nzenze was appointed Acting Executive Deputy Director. In 2023, new Centre Heads were appointed, including Dr. Jacqueline Weyer for CEZPD, Dr. Nishi Prabdial-Sing for CVI, and Dr. Mazvita Muchengeti for NCR.

6. Talent and Growth Indicators

Hiring Trends and Workforce

As of 2023, the NICD employs a team of 513 skilled individuals. The workforce consists of 73% permanent employees and 27% grant-funded or fixed-term personnel. The institution maintains a remarkably low staff turnover rate of 1.5%. The NICD, through its affiliation with the National Health Laboratory Service (NHLS), actively recruits for various roles, indicating a consistent demand for specialized scientific and public health professionals.

7. Social Media Presence and Engagement

Digital Footprint

The NICD maintains a robust digital footprint across several social media platforms, including Facebook, Instagram, LinkedIn, Twitter (X), and YouTube. These platforms are strategically utilized to disseminate critical public health information, including news, alerts, media statements, blogs, newsletters, videos, and podcasts. The institute also provides disease-specific dashboards and surveillance reports, ensuring that healthcare workers, policymakers, and the general public have access to timely and science-based information regarding communicable disease prevention. Their content often includes educational videos on important public health topics, such as measles and rabies, demonstrating a commitment to community engagement and thought leadership.

8. Recognition and Awards

Industry Recognition

The National Institute for Communicable Diseases (NICD) has garnered significant recognition for its critical contributions to public health in South Africa and the broader African continent.

The NICD is a member of the World Health Organization (WHO)-led project Vaccine Safety Net (VSN), signifying adherence to high international standards for evidence-based vaccine safety information.

Several distinguished NICD scientists have received prestigious accolades. Professor Lucille Blumberg received a South African Medical Research Council (SAMRC) Special Award for her instrumental work and outstanding contributions in the fight against