The impact of pneumococcal serotype replacement on the effectiveness of a national immunization program: a population-based active surveillance cohort study in New Zealand.

Background: In Aotearoa New Zealand (NZ) PCV7 was introduced in 2008, then PCV10 in 2011 and PCV13 in 2014. In 2017 PCV10 was re-introduced, replacing PCV13. In the present study, we investigate the resultant rapidly changing invasive pneumococcal disease (IPD) epidemiology. Methods: We compare the IPD incidence rate ratio (IRR) in NZ (2022 versus 2020) with other countries, and describe the IPD epidemiology (including trends in overall IPD and serotype 19A, and antimicrobial resistance) within NZ. Additionally, we performed a genomic-epidemiology investigation identifying the most common 19A sequence types and associated risk factors. Findings: Though IPD incidence rates have increased in the US and Australia (2021-22) after declines in 2020, in NZ the incidence rate is the highest since 2011 with a significantly higher IRR than US (p < 0.01). Incidence rates among children <2 and adults 65 or over in 2022 are the highest since 2009, driven by significant increases of serotype 19A (p = 0.01). Maori and Pacific peoples are experiencing the highest rates since 2009. Further, penicillin resistance among 19A isolates has increased from 39% (2012) to 84% (2021) (p = 0.02). Genomic sequencing identified the more virulent ST-2062 as most common among 19A isolates sequenced, increasing from 5% (2010) to 55% (2022). Interpretation: With very high incidence rates of IPD in NZ, inadequate protection against 19A, increasing resistance, and a more virulent 19A clade, targeted public health campaigns and increased PCV13 availability are needed. Funding: The NZ Ministry of Health funds IPD surveillance and typing in NZ.

Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand.

BACKGROUND: New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID-19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years. METHODS: We collected the data from multiple surveillance systems, including hospital-based severe acute respiratory infection surveillance, SHIVERS-II, -III and -IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza-like illness surveillance and SHIVERS-V sentinel GP-based ARI surveillance, SHIVERS-V traveller ARI surveillance and laboratory-based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions. RESULTS: We observed that border closure to most people, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type-1. Partial border relaxations through quarantine-free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022. CONCLUSION: Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats.

Spodoptera exigua Multiple Nucleopolyhedrovirus Increases the Susceptibility to Insecticides: A Promising Efficient Way for Pest Resistance Management.

Spodoptera exigua is a polyphagous pest of diverse crops and causes considerable economic losses. The overuse of chemical insecticides for controlling this pest results in insecticide resistance, environmental pollution and toxicity to other non-target organisms. Therefore, a sustainable and efficient way for pest management is urgently required. In this study, laboratory bioassays of eleven commonly used insecticides, the specific entomopathogen of S. exigua (Spodoptera exigua multiple nucleopolyhedrovirus, SeMNPV), and SeMNPV-insecticide combinations against the S. exigua laboratory population and two field populations were tested. Our results indicated that the two field populations had developed resistance to almost half of the tested insecticides, while SeMNPV had good virulence in all populations. Interestingly, the combined use of SeMNPV enhanced the toxicity of the tested insecticides against all populations to a different extent and considerably reduced the insecticide resistance of S. exigua field populations or even recovered the susceptibility to above insecticides. Furthermore, the field trial showed that the combined application of SeMNPV contributed to promoting the control efficacy of emamectin benzonate and chlorfenapyr. These results provide a promising efficient way for pest resistance management and an environmentally friendly approach for controlling S. exigua with the combined application of nucleopolyhedroviruses and insecticides.

Characterization of Indoxacarb Resistance in the Fall Armyworm: Selection, Inheritance, Cross-Resistance, Possible Biochemical Mechanisms, and Fitness Costs.

The fall armyworm, Spodoptera frugiperda (J.E. Smith), is a voracious insect pest that is difficult to control due to resistance to insecticides and Bt proteins. We assessed cross-resistance, resistance mechanism, and fitness costs based on the life history traits of S. frugiperda. We established an S. frugiperda strain selected for resistance to indoxacarb (Ind-SEL) from a field-collected population and an unselected strain, Ind-UNSEL. Results indicated that after 24 generations of selection, the resistance to indoxacarb was increased by 472.67-fold as compared to the Ind-UNSEL. There was high cross-resistance to deltamethrin (31.23-fold) with very low or negligible cross-resistance to chlorantraniliprole, emamectin benzoate, and/or methoxyfenozide in the Ind-SEL population. Butoxide synergist increased susceptibility to indoxacarb, indicating that P450 enzymes may be involved in indoxacarb resistance. Significantly longer developmental time of larvae extended pupal duration, shorter adult longevity, and lower fecundity were observed in Ind-SEL as compared with the Ind-UNSEL population. The Net reproductive rate (R0) was the only growth parameter that differs between crosses of Ind-SEL♂ × Ind-UNSEL♀ (176 ± 46) and Ind-SEL♀ × Ind-UNSEL♂ (328 ± 57). On the other hand, all population growth parameters differ between Ind-SEL and Ind-UNSEL strains. Our work contributes to the growing body of research that demonstrates the importance of strain genetics in fitness cost experiments and helps resistance management programs make decisions.

Comparison and Functional Analysis of Odorant-Binding Proteins and Chemosensory Proteins in Two Closely Related Thrips Species, Frankliniella occidentalis and Frankliniella intonsa (Thysanoptera: Thripidae) Based on Antennal Transcriptome Analysis.

Two closely related thrips species, Frankliniella occidentalis and Frankliniella intonsa, are important pests on agricultural and horticultural crops. They have several similarities, including occurrence patterns, host range, and aggregation pheromone compounds. However, there are very few reports about the chemosensory genes and olfactory mechanisms in these two species. To expand our knowledge of the thrips chemosensory system, we conducted antennal transcriptome analysis of two thrips species, and identified seven odorant-binding proteins (OBPs) and eight chemosensory proteins (CSPs) in F. occidentalis, as well as six OBPs and six CSPs in F. intonsa. OBPs and CSPs showed high sequence identity between the two thrips species. The RT-qPCR results showed that the orthologous genes FoccOBP1/3/4/5/6, FintOBP1/3/4/6, FoccCSP1/2/3, and FintCSP1/2 were highly expressed in male adults. Molecular docking results suggested that orthologous pairs FoccOBP4/FintOBP4, FoccOBP6/FintOBP6, and FoccCSP2/FintCSP2 might be involved in transporting the major aggregation pheromone compound neryl (S)-2-methylbutanoate, while orthologous pairs FoccOBP6/FintOBP6, FoccCSP2/FintCSP2, and FoccCSP3/FintCSP3 might be involved in transporting the minor aggregation pheromone compound (R)-lavandulyl acetate. These results will provide a fundamental basis for understanding the molecular mechanisms of pheromone reception in the two thrips species.

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

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.

Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa).

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.

Molecular characterization and functional analysis of cytochrome P450-mediated detoxification CYP302A1 gene involved in host plant adaptation in Spodoptera frugieprda.

The fall armyworm (FAW) Spodoptera frugiperda is a destructive and polyphagous pest of many essential food crops including maize and rice. The FAW is hard to manage, control, or eradicate, due to its polyphagous nature and voracity of feeding. Here, we report the characterization and functional analysis of the detoxification gene CYP302A1 and how S. frugieprda larvae use a detoxification mechanism to adapt host plants. Results demonstrated that CYP302A1 expression levels were much higher in midgut tissue and the older S. frugiperda larvae. Our current studies revealed the enhanced P450 activity in the midguts of S. frugiperda larvae after exposure to rice plants as compared to corn plants and an artificial diet. Furthermore, higher mortality was observed in PBO treated larvae followed by the exposure of rice plants as compared to the corn plant. The dsRNA-fed larvae showed downregulation of CYP302A1 gene in the midgut. At the same time, higher mortality, reduced larval weight and shorter developmental time was observed in the dsRNA-fed larvae followed by the exposure of rice plant as compared to the corn plant and DEPC-water treated plants as a control. These results concluded that the inducible P450 enzyme system and related genes could provide herbivores with an ecological opportunity to adapt to diverse host plants by utilizing secondary compounds present in their host plants.

Comprehensive Metabolome and Volatilome Analyses in Eggplant and Tomato Reveal Their Differential Responses to Tuta absoluta Infestation.

The South American tomato pinworm, Tuta absoluta, is one of the most destructive insect pests in Solanaceae crops, particularly in tomatoes. Current methods of management have proven somewhat effective but still require a more efficacious management strategy to limit its havoc on crop yield. Tomato is much more predisposed to T. absoluta as compared with other plants such as eggplants, but the underlying causes have not been fully determined. We conducted this study to unravel the volatile organic compounds (VOCs) and primary/secondary metabolites that account for the differential response of tomatoes and eggplants to T. absoluta infestation. We performed widely targeted comparative metabolome and volatilome profiling by ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and headspace solid-phase microextraction coupled to gas chromatography-mass spectrometry (HS-SPME/GC-MS), respectively, on eggplants and tomatoes under control and T. absoluta infestation conditions. Overall, 141 VOCs and 797 primary/secondary metabolites were identified, largely dominated by aldehyde, alcohols, alkanes, amine, aromatics, a heterocyclic compound, ketone, olefin, phenol, and terpenes. Most of the VOCs and primary/secondary metabolites from the terpene class were largely differentially regulated in eggplants compared with tomatoes. Eggplants emitted several compounds that were lower or completely absent in tomatoes either under control conditions or after T. absoluta infestation. The results from an electroantennogram showed that 35 differentially accumulated VOCs could elicit female T. absoluta response, implying that these volatile compounds significantly alter the behavior of this pest. These findings demonstrated that differentially accumulated metabolites and volatile compounds play major roles in eggplant resistance to T. absoluta infestation as these compounds were regulated upon attack by T. absoluta. Our findings can assist in integrated pest management efforts by developing appropriate control measures against T. absoluta in Solanaceae production.

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Behavioral and Physiological Plasticity Provides Insights into Molecular Based Adaptation Mechanism to Strain Shift in Spodoptera frugiperda.

How herbivorous insects adapt to host plants is a key question in ecological and evolutionary biology. The fall armyworm, (FAW) Spodoptera frugiperda (J.E. Smith), although polyphagous and a major pest on various crops, has been reported to have a rice and corn (maize) feeding strain in its native range in the Americas. The species is highly invasive and has recently established in China. We compared behavioral changes in larvae and adults of a corn population (Corn) when selected on rice (Rice) and the molecular basis of these adaptational changes in midgut and antennae based on a comparative transcriptome analysis. Larvae of S. frugiperda reared on rice plants continuously for 20 generations exhibited strong feeding preference for with higher larval performance and pupal weight on rice than on maize plants. Similarly, females from the rice selected population laid significantly more eggs on rice as compared to females from maize population. The most highly expressed DEGs were shown in the midgut of Rice vs. Corn. A total of 6430 DEGs were identified between the populations mostly in genes related to digestion and detoxification. These results suggest that potential adaptations for feeding on rice crops, may contribute to the current rapid spread of fall armyworm on rice crops in China and potentially elsewhere. Consistently, highly expressed DEGs were also shown in antennae; a total of 5125 differentially expressed genes (DEGs) s were identified related to the expansions of major chemosensory genes family in Rice compared to the Corn feeding population. These results not only provide valuable insight into the molecular mechanisms in host plants adaptation of S. frugiperda but may provide new gene targets for the management of this pest.

Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations.

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.

Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand.

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.

The predatory bug Orius strigicollis shows a preference for egg-laying sites based on plant topography.

BACKGROUND: Oviposition site selection is an important factor in determining the success of insect populations. Orius spp. are widely used in the biological control of a wide range of soft-bodied insect pests such as thrips, aphids, and mites. Orius strigicollis (Heteroptera: Anthocoridae) is the dominant Orius species in southern China; however, what factor drives its selection of an oviposition site after mating currently remains unknown. METHODS: Here, kidney bean pods (KBPs) were chosen as the oviposition substrate, and choice and nonchoice experiments were conducted to determine the preferences concerning oviposition sites on the KBPs of O. strigicollis. The mechanism of oviposition behavior was revealed through observation and measurement of oviposition action, the egg hatching rate, and the oviposition time. RESULTS: We found that O. strigicollis preferred the seams of the pods for oviposition, especially the seams at the tips of the KBPs. Choice and nonchoice experiments showed that females did not lay eggs when the KBP tail parts were unavailable. The rates of egg hatching on different KBP parts were not significantly different, but the time required for females to lay eggs on the tip seam was significantly lower. Decreased oviposition time is achieved on the tip seam because the insect can exploit support points found there and gain leverage for insertion of the ovipositor. DISCUSSION: The preferences for oviposition sites of O. strigicollis are significantly influenced by the topography of the KBP surface. Revealing such behavior and mechanisms will provide an important scientific basis for the mass rearing of predatory bugs.

Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand.

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.

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa).

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.

Genomic Surveillance of a Globally Circulating Distinct Group W Clonal Complex 11 Meningococcal Variant, New Zealand, 2013-2018.

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.

Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing.

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.

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand.

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.

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran.

The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.