COVID-19 OVERVIEW
Genomic surveillance was a significant component of Australia’s response to COVID-19, established in the national approach to surveillance through genomic indicators listed in the ‘Australian National Disease Surveillance Plan for COVID-19’. The CDGN supported the national COVID-19 response through a dedicated working group to monitor SARS-CoV-2 variants to inform Australia’s national approach in detecting and reporting of Variants of Concern (VOC), Variants of Interest (VOI), and Variants Under Monitoring (VUM).
CDGN VOC WORKING GROUP
The CDGN VOC Working Group is responsible for ongoing monitoring and surveillance of SARS-CoV-2 variants literature and global events to inform Australia’s national approach in detecting and reporting of Variants of Concern (VOC), Variants of Interest (VOI) and Variants Under Monitoring (VUM), and mutations of interest reported in the literature. The working group comprised of laboratory and government representatives with expertise in bioinformatics, genomic epidemiology, viral evolution, phylodynamics and medical microbiology.
The CDGN VOC Working Group regularly reviewed and updated the national VOC Laboratory Case Definition and the VOC Literature Summary to ensure the most up to date information is reflected and communicated to the public health laboratories and units. This literature summary was distributed to all jurisdictions across Australia and New Zealand through national committees, the Public Health Laboratory Network (PHLN) and the Communicable Diseases Network of Australia (CDNA). The CDGN VOC Working Group also works closely with the AusTrakka National Analysis Team to ensure timely integration of new VOCs or VOIs that are being monitored and reported in the AusTrakka National VOC reports submitted to the national, state and territory governments on a twice-weekly basis via the Australian Health Protection Principal Committee (AHPPC), PHLN and CDNA.
The CDGN VOC Working Group is still available to support ongoing SARS-CoV-2 surveillance, now shifting to convening on an as-needs basis.
Nationally aggregated sample data
The table below shows the total number of Omicron sequences in Australia categorised as variants of concern, variants of interest and variants under monitoring, as well as the number and proportion of sequences identified for each sub-lineage in the past 28 days.
Data is not equivalent to case numbers, as there may be duplicate sequences for a single case, and not all cases have samples which are able to be sequenced. Sequence numbers may vary from week to week as new sub-lineages are characterised and sequences are re-classified into these new sub-lineages.
^ the number (and percentage) of sequences within the preceding 4 week (28 day) period
~ Inclusive of all XBB* sublineages
Green boxes indicate decreases in proportion compared to previous 28-day period, whereas yellow boxes indicate increases in sequence proportion. VOI and VUMs which have not been observed in the past 8 weeks (including XBF, BR.2, BN.1, BF.7, BA.4.6, BQ.1 and BQ.1.1) have been removed from this table.
Global Overview
SARS-CoV-2 PCR percent positivity during the four-week reporting period from 24 June to 21 July 2024, as detected in integrated sentinel surveillance as part of the Global Influenza Surveillance and Response System (GISRS) and reported to FluNet, increased from 7.4% in the beginning week of the reporting period to 13.0% in the last, across 85 countries. During this period, an average of 17 358 specimens across 85 countries were tested for SARS-CoV-2 each week.
Globally, JN.1 is the most reported variant of interest (VOI), now reported by 135 countries, accounting for 25.7% of sequences in week 29, having declined from a prevalence of 30.2% in week 26. KP.3.1.1 and LB.1, both descendent lineages of JN.1 and variants under monitoring (VUMs), showed an increasing prevalence globally. They accounted for 18.6% and 9.3% of sequences in week 29 (week ending on 21 July 2024) compared to 9.4% and 7.6% in week 26, respectively. KP.3, KP.2, JN.1.7, and JN.1.18 (all VUMs) are declining. KP.3 accounted for 29.4% of sequences in week 29 compared to 32.8% in week 26 while KP.2 declined to 12.8% in week 29 from 15.3% reported in week 26.
Globally, during the 28-day period (24 June to 21 July 2024), the number of new cases and deaths increased by 30% and 26% compared to the previous 28-day period (27 May to 23 June 2024), with over 186 000 new cases reported across 96 (41%) countries and more than 2800 new fatalities reported across 35 (15%) countries, respectively. As of 21 July 2024, over 775 million confirmed cases and more than seven million deaths have been reported globally since the beginning of pandemic.
During the same period, 46 and 35 countries provided data at least once on COVID-19 hospitalizations and admissions to an intensive care unit (ICU), respectively. From the available data, over 23 000 new hospitalizations and more than 600 new ICU admissions were reported. Among the countries reporting these data consistently over the current and past reporting period, there was an overall increase of 11% and 3% in new hospitalizations and new ICU admissions, respectively.
WHO published the latest COVID-19 Vaccination Insights Report for quarter one (Jan-Mar) 2024. Globally, 9.8 million individuals received a dose of COVID-19 vaccine across 73 reporting Member States (MS) containing 22% of the global population. Among older adults, 4.9 million individuals received a dose across the 60 MS reporting on uptake in this group, corresponding to an uptake rate of 0.42% so far this year.
This global overview is taken from the latest WHO Coronavirus disease (COVID-19) Epidemiological Update.