Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand

Abstract

New Zealand’s COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from an elimination strategy to a suppression strategy and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.

Neuroinvasion and anosmia are independent phenomena upon infection with SARS-CoV-2 and its variants

“…Several mutations on the spike distinguish the different VoCs. Furthermore, some VoC isolates also present deletions in the ORF7 sequence (Jelley et al, 2022; Mazur-Panasiuk et al, 2021; Panzera et al, 2021; Pyke et al, 2021), including the Delta isolate used in the present study (deletion spanning positions 27507 to 27541 of the reference SARS-CoV-2 Wuhan genome). Since a possible link between ORF7b and olfaction loss has been proposed (Fogeron et al, 2021), we constructed a recombinant SARS-CoV-2 based on the CoV-2/W backbone, where the ORF7ab sequence was replaced by that of GFP (SARS-CoV-2 Wuhan/ΔORF7ab) (Fig.…”

“…Furthermore, besides mutations in the spike sequence in the SARS-CoV-2 variants genome, additional mutations may be present in other regions of the viral genome, including deletions in the ORF7a and ORF7b sequences (Jelley et al ., 2022; Mazur-Panasiuk et al ., 2021; Panzera et al ., 2021; Pyke et al ., 2021). ORF7a and ORF7b have been related to viral-induced apoptosis, and to interference with the innate immunity and the antiviral response (Aliyari et al, 2022; Hayn et al, 2021; Schaecher et al, 2007; Su et al, 2021), without, however, being essential to viral infection and replication (Schaecher et al, 2008; Silvas et al, 2021).…”

Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong

“…After the initial global spread of SARS-CoV-2 in 2020, new waves of infection have been triggered by the emergence of novel Variants of Concern (VOC) such as Alpha, Beta, Gamma, Delta, and most recently, Omicron and its subvariants with greater transmissibility, significant immune evasion and capacity for strong vaccine breakthrough 1 . In response to more contagious variants, countries that maintained elimination strategies throughout 2021, such as New Zealand and Singapore, pivoted towards mitigation 2 .…”

Real-time estimation of the effective reproduction number of SARS-CoV-2 in Aotearoa New Zealand

“…If case numbers are high enough for reliable inference, such fragmented outbreaks may be better modelled as separate local outbreaks, for example regional-level models for different district health boards ( Vegvari et al, 2021 ). In New Zealand’s Delta outbreak, different sub-clusters have been identified ( Jelley et al, 2022 ) but there were insufficient case numbers to fit the model for each sub-cluster separately. It is therefore not possible to disentangle the relative contributions that public health measures and compliance levels had on transmission, from other attributes of the sub-clusters dominating the outbreak at that particular point in time.…”

“…Over the following days, contact tracing and surveillance testing efforts were ramped up in an attempt to ring-fence the outbreak as daily case numbers rapidly increased to 79 new cases on 26 August. Whole genome sequencing later identified possible links to infected travellers who arrived at a managed isolation and quarantine (MIQ) facility from New South Wales, Australia ( Jelley et al, 2022 ).…”