December 2024/January 2025

Respiratory Virus Multiplex PCR and SARS-CoV-2 PCR: All Age Groups

Percentage of Specimens Positive

December 2024:

• Rhino/Enterovirus: 19.7%
• Rhinovirus: 14.4%
• SARS-CoV-2: 17.7%
• RSV: 0.8%
• Parainfluenza 1-4: 5.3%
• Human metapneumovirus: 8.1%
• Coronavirus (non-SARS-CoV-2): 3.2%
• Influenza A: 6.0%
• Influenza B: 1.8%
• Adenovirus: 5.5%
• Bordetella pertussis: 2.9%
• Bordetella parapertussis: 0.5%

January 2025:

• Rhino/Enterovirus: 24.1%
• Rhinovirus: 17.5%
• SARS-CoV-2: 21.1%
• RSV: 0.7%
• Parainfluenza 1-4: 3.3%
• Human metapneumovirus: 3.0%
• Coronavirus (non-SARS-CoV-2): 0.7%
• Influenza A: 1.8%
• Influenza B: 5.4%
• Adenovirus: 2.4%
• Bordetella pertussis: 3.0%
• Bordetella parapertussis: 0.4%

Epidemiological Weeks 1 - 5:

• SARS-CoV-2: Peaked at week 2 (23.9%), declining to 18.7% by week 5.
  • Highest positivity rates by region:
    • Limpopo: 38%
    • Mpumalanga: 29%
    • Gauteng: 21%
    • KZN: 20.9%
• Influenza A & B: Low positivity; influenza A at 2.8%, influenza B at 0.3% by week 5.
• RSV: Low positivity, at 1.1% in week 5.

Atypical Bacterial Pathogens (Weeks 1 - 5):

Weekly Cases Detected:

Bordetella pertussis:

• Weeks 1–5: 3, 2, 2, 4, 1

Mycoplasma pneumoniae:

• Weeks 1–5: 2, 3, 2, 3, 2

Chlamydia pneumoniae:

• Weeks 1–5: 1, 5, 0, 7, 12

Legionella pneumophila:

• 3 cases detected during January.

Age Distribution (Weeks 1-5):

Bordetella pertussis:

• 0–6 months: 8%
• 6–12 months: 33%
• 1–5 years: 18%
• 6–12 years: 8%
• 13–18 years: 8%
• 19–64 years: 25%

65 years: 0%

Mycoplasma pneumoniae:

• 0–6 months: 0%
• 6–12 months: 8%
• 1–5 years: 34%
• 6–12 years: 8%
• 13–18 years: 34%
• 19–64 years: 8%

65 years: 8%

Chlamydia pneumoniae:

• 0–6 months: 0%
• 6–12 months: 12%
• 1–5 years: 36%
• 6–12 years: 20%
• 13–18 years: 4%
• 19–64 years: 24%

65 years: 4%

Paediatric Respiratory Viral Multiplex PCR Data (0 – 12 years):

<1 year Age Group:

December 2024:

• Rhino/Enterovirus: 33.8%
• Rhinovirus: 21.8%
• SARS-CoV-2: 17.7%
• RSV: 2.0%
• Parainfluenza 1-4: 9.1%
• Human metapneumovirus: 4.9%
• Influenza A: 10.4%
• Influenza B: 4.6%
• Adenovirus: 7.8%

January 2025:

• Rhino/Enterovirus: 27.7%
• Rhinovirus: 23.3%
• SARS-CoV-2: 28.2%
• RSV: 2.9%
• Parainfluenza 1-4: 5.2%
• Human metapneumovirus: 1.2%
• Influenza A: 7.8%
• Influenza B: 1.9%
• Adenovirus: 10.8%

1 - 5 years Age Group:

December 2024:

• Rhino/Enterovirus: 44.8%
• Rhinovirus: 32.7%
• SARS-CoV-2: 10.7%
• RSV: 1.3%
• Parainfluenza 1-4: 11.3%
• Human metapneumovirus: 6.1%
• Influenza A: 16.4%
• Influenza B: 9.8%
• Adenovirus: 18.3%

January 2025:

• Rhino/Enterovirus: 51.9%
• Rhinovirus: 35.4%
• Enterovirus: 18.5%
• SARS-CoV-2: 14.9%
• RSV: 1.2%
• Parainfluenza 1-4: 7.3%
• Human metapneumovirus: 0.9%
• Influenza A: 15.9%
• Influenza B: 2.0%
• Adenovirus: 10.7%

6 - 12 years Age Group:

December 2024:

• Rhino/Enterovirus: 21.9%
• Rhinovirus: 15.5%
• SARS-CoV-2: 8.1%
• RSV: 0.8%
• Parainfluenza 1-4: 3.4%
• Human metapneumovirus: 2.0%
• Influenza A: 5.9%
• Influenza B: 1.5%
• Adenovirus: 8.2%

January 2025:

• Rhino/Enterovirus: 46.8%
• Rhinovirus: 25.2%
• Enterovirus: 13.4%
• SARS-CoV-2: 12.1%
• RSV: 0.2%
• Parainfluenza 1-4: 2.1%
• Human metapneumovirus: 0.3%
• Influenza A: 8.2%
• Influenza B: 0.0%
• Adenovirus: 3.6%

Significant Findings (January 2025):

• <1 year: SARS-CoV-2 (28.2%), Rhino/Enterovirus (27.7%).
• 1-5 years: Rhino/Enterovirus (51.9%), Rhinovirus (35.4%), Enterovirus (18.5%), Adenovirus (15.9%).
• 6-12 years: Rhino/Enterovirus (46.8%), Rhinovirus (25.2%), Enterovirus (13.4%).