A rising trend in COVID-19 cases and test positivity rate has been observed over the last few weeks. Data obtained from FluNet and comprise of testing done across the three sentinel surveillance programmes by the NICD

nicd.ac.za/wp-content/upl…

Flu Update For South Africa 🇿🇦

Flu continues to circulate at high levels around the country. Contrast with the 2022 flu season with the current flu season. Majority of the recent cases detected at the sentinel surveillance sites have been Influenza A(H3N2)

We are now seeing a sustained rise in COVID-19 cases in SA.

Nothing too drastic at the moment, but nevertheless, an increasing trend. We can see this growth over recent weeks more better on log scale.

Data up to 17 October '22

Influenza update for South Africa

The spike in week ending 6 Aug '22 resulted from fewer samples being submitted due to staff training. Here's the breakdown by Influenza subtype and lineage.

Early in the Influenza season, we saw mostly circulation of Influenza A(H1N1 pdm09), but this was followed by the circulation of Influenza A(H3N2) and Influenza B(Victoria).

Number of positive Influenza cases by influenza subtype and lineage across the three respiratory illnesse surveillance programmes in SA

Interesting to see H3N2 and Victoria starting to increase in prevalence. Anecdotally, I have heard of people around me experiencing flu-like symptoms. Grateful to the NICD for having such surveillance programmes 🙏🏻

Trend in new cases from all districts in Maharashtra

Hospital admissions in some European countries.

Spain, Italy and Austria below represents hospital occupancy while the rest are weekly new admissions. Hospital admissions are decreasing in some countries.

Current situation in New Zealand and Australia

Hospitalisations in Australia: Hospitalisations in New Zealand

For the period, 1st January 2020 to 1st May 2022, a total of 10 545 cases (suspected) and 362 deaths of Monkeypox were recorded in the Democratic Republic of Congo .

For 2022 alone, up to week 17, DRC has reported 1238 cases with 57 deaths. There is an issue of having laboratory-confirmed diagnosis in DRC due to limited resources, hence suspected cases are reported.

Been a while since I did an update.

COVID-19 cases continue to decline in South Africa. Current 7-day moving average is slightly above the levels seen during the interwave periods The rate of decline in cases over the last 2 months was much slower compared to similar points in time for the previous waves, possibly attributed to the rise in BA.2

As of 26 Jan '22 in SA, there are currently 5709 COVID-19 in-patients aged 12 and over.

Here are the rates based on age, vaccination status, and type of hospital care.

For current general ward patients: For current high care ward patients:

Note that there is only 1 high care ward patient in the 50-59 age group who is partially vaccinated, so you can see the rate for fully vaccinated in this age group is higher.

Current situation in the Western Cape:

Data is plotted by specimen received date up to 21 Dec '21 A welcomed slow down in the weekly growth rate in cases

Comparison of cumulative COVID-19 admissions per wave. Here the wave duration was defined from the time the country recorded a weekly incidence risk of 5 admissions per 100,000
population at the start of the wave to the same incidence risk at the end of the wave The same hospitalisation incidence risk was used in this analysis of the first two waves carried out by the NICD

thelancet.com/journals/langl…

From the latest Discovery Health data, a fully vaccinated individual has:

2 to 5x lower chances of being infected compared to an unvaccinated individual.

3 to 6x lower chances of being admitted to hospital from COVID-19 compared to an unvaccinated individual 3 to 10x lower chances of being admitted to the high care ward or ICU for COVID-19 compared to an unvaccinated individual.

At least 10x lower chances of dying from COVID-19 compared to an unvaccinated individual.

Immunocompromised patients could be potential hosts for immune-escape mutants of SARS-CoV-2

nejm.org/doi/full/10.10… Accumulation of SARS-CoV-2 variants in three persistently positive pediatric and young adult patients with hematologic malignancies.

medrxiv.org/content/10.110…

New preprint study assessing the heterologous prime-boost regime in 18 participants, whom received a first dose Covishield and then boosted 6 weeks later with Covaxin

medrxiv.org/content/10.110… "Immunogenicity profile against Alpha, Beta and Delta variants in heterologous group was superior and IgG antibody and neutralising antibody response of the participants was also significantly higher compared to that in the homologous groups"

Rt > 1 once again in India. A slight uptick in cases was observed over the past week.

Source: OWID

Greece have seen a sharp spike in cases over the past week, with low prevalence of Delta. The likely culprit is B.1.1.318, a variant under investigation (VUI)

Image: outbreak.info B.1.1.318 has recently increased in prevalence in Greece, and was the dominant variant in genomic sequencing performed during June.

Image: outbreak.info

The estimated effective reproduction number for SARS-CoV-2 in India is currently 0.92.

unsupervised.online/static/covid-1… Rt has been on the increase for the past few weeks

Although first identified in Peru, Lambda's most sequences on GISAID have come from Chile (840). However, it has not managed to outcompete Gamma in that region. Cases are declining in Chile. They have fully vaccinated over 54% of their population. There are no sequences for Lambda in SA, but this not imply that Lambda is not here. It could be a case or two that won't be picked up by random sampling through genomic surveillance. We have not detected Gamma here as yet, but likely has already been introduced into SA

Some more Delta sequences are now reflected on GISAID. In total 281 sequences of Delta have be detected through genomic surveillance in SA Here, we can clearly see that Delta is driving our infections in the country