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

Jelley, Lauren; Douglas, Jordan; Ren, Xiaoyun; Winter, David J.; McNeill, Andrea; Huang, Q. Sue; French, Nigel P.; Welch, David; Hadfield, James; Ligt, Joep de; Geoghegan, Jemma L.

doi:10.1038/s41467-022-31784-5

Cited by 18 publications

(19 citation statements)

References 55 publications

(69 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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 .…”

Section: Introductionmentioning

confidence: 99%

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

Xie

Edwards

Adam

et al. 2022

Preprint

View full text Add to dashboard Cite

After keeping infections at bay for two years, Hong Kong experienced a surge of Omicron BA.2 infections in early 2022 that overwhelmed the health care system, isolation facilities, and contact tracing capacity, leading to one of the highest per-capita death rates of COVID-19 in early 2022. The outbreak occurred against a backdrop of a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures. Using genome sequences and epidemiological data from this time, we reconstruct the epidemic trajectory of the BA.2 wave, estimate transmission and incidence rates, and evaluate the effectiveness of policy changes. We identify an increase in the effective reproductive rate (Re) to 9.5 in mid-January 2022, which preceded real-time estimates of transmission (Rt), revealing that BA.2 community transmission was under-ascertained weeks before the epidemic appeared to surge in mid-February 2022. Due to this, public health measures were relaxed in early February (Spring Festival) while Re increased and remained > 1 throughout February. An independent estimation of point prevalence and incidence using phylodynamics also indicates extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. This study demonstrates that relying on Rt estimation methods dependent on case reporting can misinform epidemic response planning, sometimes with substantial consequences. There is a need for future research and implementation of improved estimates of epidemic growth in near real-time that combine multiple disparate data sources to better inform outbreak response policy.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Xie

Edwards

Adam

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…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.…”

Section: Resultsmentioning

confidence: 89%

“…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).…”

Section: Discussionmentioning

confidence: 99%

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

Melo

Perraud

Alvarez

et al. 2022

Preprint

View full text Add to dashboard Cite

Anosmia was identified as a hallmark of COVID-19 early in the pandemic, however, with the emergence of variants of concern, the clinical profile induced by SARS-CoV-2 infection has changed, with anosmia being less frequent. Several studies have focused on the neuropathogenesis of the original SARS-CoV-2, but little is known about the neuropathological potential of the variants. Here, we assessed the clinical, olfactory and inflammatory conditions of golden hamsters infected with the original SARS-CoV-2, its ORF7-deleted mutant, and three variants: Gamma, Delta and Omicron/BA.1. We show that infected animals developed a variant-dependent clinical disease, and that the ORF7 of SARS-CoV-2 contribute to causing olfactory disturbances. Conversely, all SARS-CoV-2 variants were found to be neuroinvasive, regardless of the clinical presentation they induce. With newly-generated nanoluciferase-expressing SARS-CoV-2, we validated the olfactory pathway as a main entry point towards the brain, confirming that neuroinvasion and anosmia are independent phenomena upon SARS-CoV-2 infection.

show abstract

“…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.…”

Section: Discussionmentioning

confidence: 99%

“…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 ).…”

Section: Introductionmentioning

confidence: 99%

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

Binny

Lustig

Hendy

et al. 2022

PeerJ

View full text Add to dashboard Cite

During an epidemic, real-time estimation of the effective reproduction number supports decision makers to introduce timely and effective public health measures. We estimate the time-varying effective reproduction number, Rt, during Aotearoa New Zealand’s August 2021 outbreak of the Delta variant of SARS-CoV-2, by fitting the publicly available EpiNow2 model to New Zealand case data. While we do not explicitly model non-pharmaceutical interventions or vaccination coverage, these two factors were the leading drivers of variation in transmission in this period and we describe how changes in these factors coincided with changes in Rt. Alert Level 4, New Zealand’s most stringent restriction setting which includes stay-at-home measures, was initially effective at reducing the median Rtto 0.6 (90% CrI 0.4, 0.8) on 29 August 2021. As New Zealand eased certain restrictions and switched from an elimination strategy to a suppression strategy, Rt subsequently increased to a median 1.3 (1.2, 1.4). Increasing vaccination coverage along with regional restrictions were eventually sufficient to reduce Rtbelow 1. The outbreak peaked at an estimated 198 (172, 229) new infected cases on 10 November, after which cases declined until January 2022. We continue to update Rtestimates in real time as new case data become available to inform New Zealand’s ongoing pandemic response.

show abstract

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

Cited by 18 publications

References 55 publications

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

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

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

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

Contact Info

Product

Resources

About