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, R
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.
The strategy in New Zealand (Aotearoa) to eliminate coronavirus disease requires that international arrivals undergo managed isolation and quarantine and mandatory testing for severe acute ...respiratory syndrome coronavirus 2. Combining genomic and epidemiologic data, we investigated the origin of an acute case of coronavirus disease identified in the community after the patient had spent 14 days in managed isolation and quarantine and had 2 negative test results. By combining genomic sequence analysis and epidemiologic investigations, we identified a multibranched chain of transmission of this virus, including on international and domestic flights, as well as a probable case of aerosol transmission without direct person-to-person contact. These findings show the power of integrating genomic and epidemiologic data to inform outbreak investigations.
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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.
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In New Zealand, international arrivals are quarantined and undergo severe acute respiratory syndrome coronavirus 2 screening; those who test positive are transferred to a managed isolation facility ...(MIF). Solo traveler A and person E from a 5-person travel group (BCDEF) tested positive. After transfer to the MIF, person A and group BCDEF occupied rooms >2 meters apart across a corridor. Persons B, C, and D subsequently tested positive; viral sequences matched A and were distinct from E. The MIF was the only shared location of persons A and B, C, and D, and they had no direct contact. Security camera footage revealed 4 brief episodes of simultaneous door opening during person A's infectious period. This public health investigation demonstrates transmission from A to B, C, and D while in the MIF, with airborne transmission the most plausible explanation. These findings are of global importance for coronavirus disease public health interventions and infection control practices.
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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.
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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.
Genomic surveillance is an essential part of effective disease control, enabling identification of emerging and expanding strains and monitoring of subsequent interventions. Whole-genome sequencing ...was used to analyze the genomic diversity of all Neisseria meningitidis isolates submitted to the New Zealand Meningococcal Reference Laboratory during 2013-2018. Of the 347 isolates submitted for whole-genome sequencing, we identified 68 sequence types belonging to 18 clonal complexes (CC). The predominant CC was CC41/44; next in predominance was CC11. Comparison of the 45 New Zealand group W CC11 isolates with worldwide representatives of group W CC11 isolates revealed that the original UK strain, the 2013 UK strain, and a distinctive variant (the 2015 strain) were causing invasive group W meningococcal disease in New Zealand. The 2015 strain also demonstrated increased resistance to penicillin and has been circulating in Canada and several countries in Europe, highlighting that close monitoring is needed to prevent future outbreaks around the world.
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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.
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Maize is moderately sensitive to salt stress; therefore, soil salinity is a serious threat to its production worldwide. Here, excellent salt-tolerant maize inbred line TL1317 and extremely ...salt-sensitive maize inbred line SL1303 were screened to understand the maize response to salt stress and its tolerance mechanisms. Relative water content, membrane stability index, stomatal conductance, chlorophyll content, maximum photochemical efficiency, photochemical efficiency, shoot and root fresh/dry weight, and proline and water soluble sugar content analyses were used to identify that the physiological effects of osmotic stress of salt stress were obvious and manifested at about 3 days after salt stress in maize. Moreover, the ion concentration of two maize inbred lines revealed that the salt-tolerant maize inbred line could maintain low Na
concentration by accumulating Na
in old leaves and gradually shedding them to exclude excessive Na
. Furthermore, the K
uptake and retention abilities of roots were important in maintaining K
homeostasis for salt tolerance in maize. RNA-seq and qPCR results revealed some Na
/H
antiporter genes and Ca
transport genes were up-regulated faster and higher in TL1317 than those in SL1303. Some K
transport genes were down-regulated in SL1303 but up-regulated in TL1317. RNA-seq results, along with the phenotype and physiological results, suggested that the salt-tolerant maize inbred line TL1317 possesses more rapidly and effectively responses to remove toxic Na
ions and maintain K
under salt stress than the salt-sensitive maize inbred line SL1303. This response should facilitate cell homoeostasis under salt stress and result in salt tolerance in TL1317.
Western flower thrips (WFT),
(Pergande), is a highly invasive pest, infesting many species of plants worldwide, but few studies have investigated the visual and olfactory cues associated with their ...foraging behaviors. In this study, the distance traveled by WFT to locate yellow cards using only visual cues and visual cues plus olfactory cues was studied first. Subsequently, preferences for colors (white, red, green, purple, yellow and blue) and patterns (triangle, rectangle, circle and flower-shape) over short distances were assessed with free-choice tests. Finally, as yellow was the most efficient color to catch WFT under laboratory conditions, the yellow flower-shape was used as the visual cue, and preferences between visual and olfactory cues were evaluated with dual choice tests. The results showed that the capture rate of WFT by visual cues decreased as selection distance increased, however capture rate remained higher with the addition of olfactory cues. The flower shape attracted the greatest number of WFT among all shapes tested. The combination of visual cues and extracted volatiles from flowering
L. attracted higher numbers of WFT than to the olfactory cues alone, however these were similar to visual cues alone. The presence of olfactory cues resulted in higher residence times by WFT than did the absence of olfactory cues. These results show the relative effects of visual and olfactory cues on the orientation of WFT to hosts and highlight that visual cues dominate selection behavior at short distances. These findings can be used in the development of efficient trapping products and management strategies for thrips.
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