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1.
Viruses ; 14(4)2022 03 25.
Article in English | MEDLINE | ID: covidwho-1820404

ABSTRACT

Recent research using UV radiation with wavelengths in the 200-235 nm range, often referred to as far-UVC, suggests that the minimal health hazard associated with these wavelengths will allow direct use of far-UVC radiation within occupied indoor spaces to provide continuous disinfection. Earlier experimental studies estimated the susceptibility of airborne human coronavirus OC43 exposed to 222-nm radiation based on fitting an exponential dose-response curve to the data. The current study extends the results to a wider range of doses of 222 nm far-UVC radiation and uses a computational model coupling radiation transport and computational fluid dynamics to improve dosimetry estimates. The new results suggest that the inactivation of human coronavirus OC43 within our exposure system is better described using a bi-exponential dose-response relation, and the estimated susceptibility constant at low doses-the relevant parameter for realistic low dose rate exposures-was 12.4 ± 0.4 cm2/mJ, which described the behavior of 99.7% ± 0.05% of the virus population. This new estimate is more than double the earlier susceptibility constant estimates that were based on a single-exponential dose response. These new results offer further evidence as to the efficacy of far-UVC to inactivate airborne pathogens.


Subject(s)
COVID-19 , Coronavirus OC43, Human , Disinfection/methods , Humans , SARS-CoV-2 , Ultraviolet Rays , Virus Inactivation
2.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-332911

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 elimination to suppression and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.

3.
Viruses ; 14(4):684, 2022.
Article in English | MDPI | ID: covidwho-1762725

ABSTRACT

Recent research using UV radiation with wavelengths in the 200–235 nm range, often referred to as far-UVC, suggests that the minimal health hazard associated with these wavelengths will allow direct use of far-UVC radiation within occupied indoor spaces to provide continuous disinfection. Earlier experimental studies estimated the susceptibility of airborne human coronavirus OC43 exposed to 222-nm radiation based on fitting an exponential dose–response curve to the data. The current study extends the results to a wider range of doses of 222 nm far-UVC radiation and uses a computational model coupling radiation transport and computational fluid dynamics to improve dosimetry estimates. The new results suggest that the inactivation of human coronavirus OC43 within our exposure system is better described using a bi-exponential dose–response relation, and the estimated susceptibility constant at low doses-the relevant parameter for realistic low dose rate exposures-was 12.4 ±0.4 cm2/mJ, which described the behavior of 99.7% ±0.05% of the virus population. This new estimate is more than double the earlier susceptibility constant estimates that were based on a single-exponential dose response. These new results offer further evidence as to the efficacy of far-UVC to inactivate airborne pathogens.

4.
Sci Rep ; 12(1): 4373, 2022 03 23.
Article in English | MEDLINE | ID: covidwho-1758367

ABSTRACT

Many infectious diseases, including COVID-19, are transmitted by airborne pathogens. There is a need for effective environmental control measures which, ideally, are not reliant on human behaviour. One potential solution is Krypton Chloride (KrCl) excimer lamps (often referred to as Far-UVC), which can efficiently inactivate pathogens, such as coronaviruses and influenza, in air. Research demonstrates that when KrCl lamps are filtered to remove longer-wavelength ultraviolet emissions they do not induce acute reactions in the skin or eyes, nor delayed effects such as skin cancer. While there is laboratory evidence for Far-UVC efficacy, there is limited evidence in full-sized rooms. For the first time, we show that Far-UVC deployed in a room-sized chamber effectively inactivates aerosolised Staphylococcus aureus. At a room ventilation rate of 3 air-changes-per-hour (ACH), with 5 filtered-sources the steady-state pathogen load was reduced by 98.4% providing an additional 184 equivalent air changes (eACH). This reduction was achieved using Far-UVC irradiances consistent with current American Conference of Governmental Industrial Hygienists threshold limit values for skin for a continuous 8-h exposure. Our data indicate that Far-UVC is likely to be more effective against common airborne viruses, including SARS-CoV-2, than bacteria and should thus be an effective and "hands-off" technology to reduce airborne disease transmission. The findings provide room-scale data to support the design and development of effective Far-UVC systems.


Subject(s)
COVID-19 , Staphylococcal Infections , Disinfection , Humans , SARS-CoV-2 , Ultraviolet Rays
5.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-309856

ABSTRACT

Many infectious diseases, including COVID-19, are transmitted by airborne pathogens. There is a need for effective environmental control measures which, ideally, are not reliant on human behaviour. One potential solution is Far-UVC which can efficiently inactivate pathogens, such as coronaviruses and influenza, in air. When appropriately filtered, and because of its limited penetration, there is evidence that Far-UVC does not induce acute reactions in the skin or eyes, nor delayed effects such as skin cancer. While there is laboratory evidence for far-UVC efficacy, there is limited evidence in full-sized rooms. In the first study of its type, we show that Far-UVC deployed in a room-sized chamber effectively inactivates aerosolised Staphylococcus aureus . At a room ventilation rate of 3 air changes per hour (ACH), with 5 filtered sources the steady-state pathogen load was reduced by 92.1% providing an additional 35 equivalent air changes (eACH). This reduction was achieved using Far-UVC intensities consistent with current regulatory limits. Far-UVC is likely to be more effective against common airborne viruses, including SARS-CoV-2, and should thus be an effective and “hands-off” technology to reduce airborne disease transmission. The findings provide room-scale data to support the design and development of safe and effective Far-UVC systems.

6.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-307474

ABSTRACT

A direct approach to limit airborne transmission of pathogens is to inactivate them within a short time of their production. Germicidal ultraviolet light (UV), typically at 254 nm, is effective in this context, but it is a health hazard to the skin and eyes. By contrast, far-UVC light (207-222 nm) efficiently kills pathogens without harm to exposed human cells or tissues. We previously demonstrated that 222-nm UV light efficiently kills airborne influenza virus (H1N1);here we extend the far-UVC studies to explore efficacy against human coronaviruses from subgroups alpha (HCoV-229E) and beta (HCoV-OC43). We found that low doses of, respectively 1.7 and 1.2 mJ/cm 2 inactivated 99.9% of aerosolized alpha coronavirus 229E and beta coronavirus OC43. Based on these results for the beta HCoV-OC43 coronavirus, continuous far-UVC exposure in public locations at the currently recommended exposure limit (3 mJ/cm 2 /hour) would result in 99.9% viral inactivation in ~ 25 minutes. Increasing the far- UVC intensity by, say, a factor of 2 would halve these disinfection times, while still maintaining safety. As all human coronaviruses have similar genomic size, a key determinant of radiation sensitivity, it is realistic to expect that far-UVC light will show comparable inactivation efficiency against other human coronaviruses, including SARS-CoV-2.

7.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-325912

ABSTRACT

PEACH Tree is an easy-to-use, online tool for displaying multiple sequence alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for rapidly tracing evolutionary and transmission histories by filtering invariant sites out of the display, and allowing samples to readily be filtered out of the display. These features, coupled with the ability to display epidemiological metadata, make the tool suitable for infectious disease epidemiology. PEACH Tree further enables much needed communication between the fields of genomics and infectious disease epidemiology, as exemplified by the COVID-19 pandemic.

8.
Sci Rep ; 11(1): 19930, 2021 10 07.
Article in English | MEDLINE | ID: covidwho-1462026

ABSTRACT

Transmission of SARS-CoV-2 by aerosols has played a significant role in the rapid spread of COVID-19 across the globe. Indoor environments with inadequate ventilation pose a serious infection risk. Whilst vaccines suppress transmission, they are not 100% effective and the risk from variants and new viruses always remains. Consequently, many efforts have focused on ways to disinfect air. One such method involves use of minimally hazardous 222 nm far-UVC light. Whilst a small number of controlled experimental studies have been conducted, determining the efficacy of this approach is difficult because chamber or room geometry, and the air flow within them, influences both far-UVC illumination and aerosol dwell times. Fortunately, computational multiphysics modelling allows the inadequacy of dose-averaged assessment of viral inactivation to be overcome in these complex situations. This article presents the first validation of the WYVERN radiation-CFD code for far-UVC air-disinfection against survival fraction measurements, and the first measurement-informed modelling approach to estimating far-UVC susceptibility of viruses in air. As well as demonstrating the reliability of the code, at circa 70% higher, our findings indicate that aerosolized human coronaviruses are significantly more susceptible to far-UVC than previously thought.


Subject(s)
Coronavirus 229E, Human/radiation effects , Coronavirus Infections/prevention & control , Coronavirus OC43, Human/radiation effects , Disinfection/methods , Ultraviolet Rays , Virus Inactivation/radiation effects , Aerosols/isolation & purification , Air Microbiology , COVID-19/prevention & control , Computer Simulation , Coronavirus 229E, Human/isolation & purification , Coronavirus 229E, Human/physiology , Coronavirus OC43, Human/isolation & purification , Coronavirus OC43, Human/physiology , Disinfection/instrumentation , Equipment Design , Humans , Models, Biological
10.
Virus Evol ; 7(2): veab052, 2021.
Article in English | MEDLINE | ID: covidwho-1412220

ABSTRACT

New Zealand, Australia, Iceland, and Taiwan all saw success in controlling their first waves of Coronavirus Disease 2019 (COVID-19). As islands, they make excellent case studies for exploring the effects of international travel and human movement on the spread of COVID-19. We employed a range of robust phylodynamic methods and genome subsampling strategies to infer the epidemiological history of Severe acute respiratory syndrome coronavirus 2 in these four countries. We compared these results to transmission clusters identified by the New Zealand Ministry of Health by contact tracing strategies. We estimated the effective reproduction number of COVID-19 as 1-1.4 during early stages of the pandemic and show that it declined below 1 as human movement was restricted. We also showed that this disease was introduced many times into each country and that introductions slowed down markedly following the reduction of international travel in mid-March 2020. Finally, we confirmed that New Zealand transmission clusters identified via standard health surveillance strategies largely agree with those defined by genomic data. We have demonstrated how the use of genomic data and computational biology methods can assist health officials in characterising the epidemiology of viral epidemics and for contact tracing.

11.
Emerg Infect Dis ; 27(9): 2361-2368, 2021 09.
Article in English | MEDLINE | ID: covidwho-1369634

ABSTRACT

Since severe acute respiratory syndrome coronavirus 2 was first eliminated in New Zealand in May 2020, a total of 13 known coronavirus disease (COVID-19) community outbreaks have occurred, 2 of which led health officials to issue stay-at-home orders. These outbreaks originated at the border via isolating returnees, airline workers, and cargo vessels. Because a public health system was informed by real-time viral genomic sequencing and complete genomes typically were available within 12 hours of community-based positive COVID-19 test results, every outbreak was well-contained. A total of 225 community cases resulted in 3 deaths. Real-time genomics were essential for establishing links between cases when epidemiologic data could not do so and for identifying when concurrent outbreaks had different origins.


Subject(s)
COVID-19 , Viruses , Genomics , Humans , New Zealand/epidemiology , SARS-CoV-2
12.
Lancet Reg Health West Pac ; 15: 100256, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1364342

ABSTRACT

Background: COVID-19 elimination measures, including border closures have been applied in New Zealand. We have modelled the potential effect of vaccination programmes for opening borders. Methods: We used a deterministic age-stratified Susceptible, Exposed, Infectious, Recovered (SEIR) model. We minimised spread by varying the age-stratified vaccine allocation to find the minimum herd immunity requirements (the effective reproduction number Reff<1 with closed borders) under various vaccine effectiveness (VE) scenarios and R0 values. We ran two-year open-border simulations for two vaccine strategies: minimising Reff and targeting high-risk groups. Findings: Targeting of high-risk groups will result in lower hospitalisations and deaths in most scenarios. Reaching the herd immunity threshold (HIT) with a vaccine of 90% VE against disease and 80% VE against infection requires at least 86•5% total population uptake for R0=4•5 (with high vaccination coverage for 30-49-year-olds) and 98•1% uptake for R0=6. In a two-year open-border scenario with 10 overseas cases daily and 90% total population vaccine uptake (including 0-15 year olds) with the same vaccine, the strategy of targeting high-risk groups is close to achieving HIT, with an estimated 11,400 total hospitalisations (peak 324 active and 36 new daily cases in hospitals), and 1,030 total deaths. Interpretation: Targeting high-risk groups for vaccination will result in fewer hospitalisations and deaths with open borders compared to targeting reduced transmission. With a highly effective vaccine and a high total uptake, opening borders will result in increasing cases, hospitalisations, and deaths. Other public health and social measures will still be required as part of an effective pandemic response. Funding: This project was funded by the Health Research Council [20/1018]. Research in context.

14.
Emerg Infect Dis ; 27(5): 1317-1322, 2021 05.
Article in English | MEDLINE | ID: covidwho-1202381

ABSTRACT

Real-time genomic sequencing has played a major role in tracking the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contributing greatly to disease mitigation strategies. In August 2020, after having eliminated the virus, New Zealand experienced a second outbreak. During that outbreak, New Zealand used genomic sequencing in a primary role, leading to a second elimination of the virus. We generated genomes from 78% of the laboratory-confirmed samples of SARS-CoV-2 from the second outbreak and compared them with the available global genomic data. Genomic sequencing rapidly identified that virus causing the second outbreak in New Zealand belonged to a single cluster, thus resulting from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data. Access to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.


Subject(s)
COVID-19 , SARS-CoV-2 , Disease Outbreaks , Genomics , Humans , New Zealand/epidemiology
15.
Emerg Infect Dis ; 27(3): 687-693, 2021 03.
Article in English | MEDLINE | ID: covidwho-1007034

ABSTRACT

Since the first wave of coronavirus disease in March 2020, citizens and permanent residents returning to New Zealand have been required to undergo managed isolation and quarantine (MIQ) for 14 days and mandatory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of October 20, 2020, of 62,698 arrivals, testing of persons in MIQ had identified 215 cases of SARS-CoV-2 infection. Among 86 passengers on a flight from Dubai, United Arab Emirates, that arrived in New Zealand on September 29, test results were positive for 7 persons in MIQ. These passengers originated from 5 different countries before a layover in Dubai; 5 had negative predeparture SARS-CoV-2 test results. To assess possible points of infection, we analyzed information about their journeys, disease progression, and virus genomic data. All 7 SARS-CoV-2 genomes were genetically identical, except for a single mutation in 1 sample. Despite predeparture testing, multiple instances of in-flight SARS-CoV-2 transmission are likely.


Subject(s)
Aircraft , COVID-19 , Quarantine , SARS-CoV-2/isolation & purification , COVID-19/diagnosis , COVID-19/transmission , Humans , Masks , New Zealand , Physical Distancing , SARS-CoV-2/classification , United Arab Emirates
16.
Nat Commun ; 11(1): 6351, 2020 12 11.
Article in English | MEDLINE | ID: covidwho-974936

ABSTRACT

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide 'lockdown' of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected during the 'first wave', representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re of New Zealand's largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.


Subject(s)
COVID-19/epidemiology , Genome, Viral/genetics , Genomics/methods , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/virology , Child , Child, Preschool , Female , Geography , Humans , Infant , Infant, Newborn , Male , Middle Aged , New Zealand/epidemiology , Pandemics , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/physiology , Whole Genome Sequencing/methods , Young Adult
17.
Sci Rep ; 10(1): 10285, 2020 06 24.
Article in English | MEDLINE | ID: covidwho-617064

ABSTRACT

A direct approach to limit airborne viral transmissions is to inactivate them within a short time of their production. Germicidal ultraviolet light, typically at 254 nm, is effective in this context but, used directly, can be a health hazard to skin and eyes. By contrast, far-UVC light (207-222 nm) efficiently kills pathogens potentially without harm to exposed human tissues. We previously demonstrated that 222-nm far-UVC light efficiently kills airborne influenza virus and we extend those studies to explore far-UVC efficacy against airborne human coronaviruses alpha HCoV-229E and beta HCoV-OC43. Low doses of 1.7 and 1.2 mJ/cm2 inactivated 99.9% of aerosolized coronavirus 229E and OC43, respectively. As all human coronaviruses have similar genomic sizes, far-UVC light would be expected to show similar inactivation efficiency against other human coronaviruses including SARS-CoV-2. Based on the beta-HCoV-OC43 results, continuous far-UVC exposure in occupied public locations at the current regulatory exposure limit (~3 mJ/cm2/hour) would result in ~90% viral inactivation in ~8 minutes, 95% in ~11 minutes, 99% in ~16 minutes and 99.9% inactivation in ~25 minutes. Thus while staying within current regulatory dose limits, low-dose-rate far-UVC exposure can potentially safely provide a major reduction in the ambient level of airborne coronaviruses in occupied public locations.


Subject(s)
Antiviral Agents/adverse effects , Betacoronavirus/radiation effects , Disinfection/methods , Ultraviolet Rays/adverse effects , Virus Inactivation/radiation effects , COVID-19 , Cell Line , Coronavirus 229E, Human/radiation effects , Coronavirus Infections/radiotherapy , Coronavirus OC43, Human/radiation effects , Humans , Pandemics , Particulate Matter/radiation effects , Pneumonia, Viral/radiotherapy , SARS Virus/radiation effects , SARS-CoV-2
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