Area-level geographic and socioeconomic factors and the local incidence of SARS-CoV-2 infections in Queensland between 2020 and 2022.

OBJECTIVE: Calculate the incidence of SARS-CoV-2 (COVID-19) infection notifications and the influence of area-level geographic and socioeconomic factors in Queensland using real-time data from the COVID-19 Real-time Information System for Preparedness and Epidemic Response (CRISPER) project. DESIGN AND SETTING: Population-level ecological study and spatial mapping of the incidence of COVID-19 infection notifications in Queensland, by postcode, 2020-2022. MAIN OUTCOME MEASURES: Proportions and distribution of COVID-19 infection notifications by year, age-group, socioeconomic disadvantage, and geospatial mapping. Incidence rate ratios (IRRs) were calculated. RESULTS: Between 28 January 2020 and 30 June 2022, a total of 609,569 cases of COVID-19 associated with a Queensland postcode were recorded. The highest proportion of cases occurred in 2022 (96.5%), and in the 20- to 24-year age category (IRR = 1.787). In non-Major City areas, there was also a higher incidence of COVID-19 cases in lower socioeconomic areas (IRR = 0.84) than in higher socioeconomic areas (IRR = 0.66). CONCLUSIONS: Queensland experienced its highest proportion of COVID-19 cases once domestic and international borders opened. However, geographic and socioeconomic factors may have still contributed to a higher incidence of COVID-19 cases across some Queensland areas. IMPLICATIONS FOR PUBLIC HEALTH: Although Australia has moved from the emergency response phase of the COVID-19 pandemic, we need to ensure ongoing prevention strategies target groups and areas that we have identified with the highest incidence.

Gastropod first intermediate hosts for two species of Monorchiidae Odhner, 1911 (Trematoda): I can't believe it's not bivalves!

The trematode superfamily Monorchioidea comprises three families of teleost parasites: the Monorchiidae Odhner, 1911, Lissorchiidae Magath, 1917, and Deropristidae Cable & Hunninen, 1942. All presently known lissorchiid and deropristid life cycles have gastropods as first intermediate hosts, whereas those of monorchiids involve bivalves. Here, we report an unexpected intermediate host for monorchiids; two species of Hurleytrematoides Yamaguti, 1954 use gastropods as first intermediate hosts. Sporocysts and cercariae were found infecting two species of the family Vermetidae, highly specialised sessile gastropods that form calcareous tubes, from two locations off the coast of Queensland, Australia. These intramolluscan infections broadly corresponded morphologically to those of known monorchiids in that the cercariae have a spinous tegument, oral and ventral suckers, a simple tail and distinct eye-spots. Given the simplified morphology of intramolluscan infections, genetic data provided a definitive identification. ITS2 rDNA and cox1 mtDNA sequence data from the gastropod infections were identical to two species of Hurleytrematoides, parasites of butterflyfishes (Chaetodontidae); Hurleytrematoides loi McNamara & Cribb, 2011 from Moreton Bay (south-eastern Queensland) and Heron Island (southern Great Barrier Reef) and Hurleytrematoides morandi McNamara & Cribb, 2011 from Heron Island. Notably, species of Hurleytrematoides are positioned relatively basal in the phylogeny of the Monorchiidae and are a sister lineage to that of species known to infect bivalves. Thus, the most parsimonious evolutionary hypothesis to explain infection of gastropods by these monorchiids is that basal monorchiids (in our analyses, species of Cableia Sogandares-Bernal, 1959, Helicometroides Yamaguti, 1934 and Hurleytrematoides) will all prove to infect gastropods, suggesting a single host switching event into bivalves for more derived monorchiids (17 other genera in our phylogenetic analyses). A less parsimonious hypothesis is that the infection of vermetids will prove to be restricted to species of Hurleytrematoides, as an isolated secondary recolonisation of gastropods from a bivalve-infecting lineage. Regardless of how their use arose, vermetids represent a dramatic host jump relative to the rest of the Monorchiidae, one potentially enabled by their specialised feeding biology.

Seasonal temperature, the lunar cycle and diurnal rhythms interact in a combinatorial manner to modulate genomic responses to the environment in a reef-building coral.

Rhythms of various periodicities drive cyclical processes in organisms ranging from single cells to the largest mammals on earth, and on scales from cellular physiology to global migrations. The molecular mechanisms that generate circadian behaviours in model organisms have been well studied, but longer phase cycles and interactions between cycles with different periodicities remain poorly understood. Broadcast spawning corals are one of the best examples of an organism integrating inputs from multiple environmental parameters, including seasonal temperature, the lunar phase and hour of the day, to calibrate their annual reproductive event. We present a deep RNA-sequencing experiment utilizing multiple analyses to differentiate transcriptomic responses modulated by the interactions between the three aforementioned environmental parameters. Acropora millepora was sampled over multiple 24-hr periods throughout a full lunar month and at two seasonal temperatures. Temperature, lunar and diurnal cycles produce distinct transcriptomic responses, with interactions between all three variables identifying a core set of genes. These core genes include mef2, a developmental master regulator, and two heterogeneous nuclear ribonucleoproteins, one of which is known to post-transcriptionally interact with mef2 and with biological clock-regulating mRNAs. Interactions between diurnal and temperature differences impacted a range of core processes ranging from biological clocks to stress responses. Genes involved with developmental processes and transcriptional regulation were impacted by the lunar phase and seasonal temperature differences. Lastly, there was a diurnal and lunar phase interaction in which genes involved with RNA-processing and translational regulation were differentially regulated. These data illustrate the extraordinary levels of transcriptional variation across time in a simple radial cnidarian in response to the environment under normal conditions.

Intermediate host switches drive diversification among the largest trematode family: evidence from the Polypipapiliotrematinae n. subf. (Opecoelidae), parasites transmitted to butterflyfishes via predation of coral polyps.

Podocotyloides stenometra Pritchard, 1966 (Digenea: Opecoelidae) is the only trematode known to infect anthozoan corals. It causes disease in coral polyps of the genus Porites Link (Scleractinia: Poritidae) and its life-cycle depends on ingestion of these polyps by butterflyfishes (Perciformes: Chaetodontidae). This species has been reported throughout the Indo-Pacific, from the Seychelles to the Galápagos, but no study has investigated whether multiple species are involved. Here, we recollect P. stenometra from its type-host and type-locality, in Hawaiian waters, and describe four new species from examination of 768 butterflyfishes from French Polynesia. On the basis of morphology, phylogeny and life-history, we propose Polypipapiliotrema Martin, Cutmore & Cribb n. gen. and the Polypipapiliotrematinae Martin, Cutmore & Cribb n. subf., for P. stenometra (Pritchard) n. comb., P. citerovarium Martin, Cutmore & Cribb n. sp., P. hadrometra Martin, Cutmore & Cribb n. sp., P. heniochi Martin, Cutmore & Cribb n. sp., and P. ovatheculum Martin, Cutmore & Cribb n. sp. Given the diversity uncovered here and the ubiquity, abundance and diversity of butterflyfishes on coral reefs, we predict that Polypipapiliotrema will prove to comprise a rich complex of species causing disease in corals across the Indo-Pacific. The unique life-cycle of these taxa is consistent with phylogenetic distinction of the group and provides evidence for a broader basis of diversification among the family. We argue that life-cycle specialisation, in terms of adoption of disparate second intermediate host groups, has been a key driver of the diversification and richness of the Opecoelidae, the largest of all trematode families and the group most frequently encountered in coral reef fishes.

An updated concept and revised composition for Hamacreadium Linton, 1910 (Opecoelidae: Plagioporinae) clarifies a previously obscured pattern of host-specificity among species.

The present concept of the trematode genus Hamacreadium Linton, 1910 encompasses considerable morphological variability and includes species reported from a broad range of fishes. These include herbivores and planktivores, despite the life-cycle of the type-species, Hamacreadium mutabile Linton, 1910, being known to use fishes as intermediate hosts. Reports of H. mutabile are numerous, spanning the west Atlantic, east Pacific and Indo-west Pacific, whereas other nominal species are infrequently reported and several inadequately described. Following a comprehensive review, a strict revised morphological definition is proposed for the genus. Several nominal species are excluded, but, conversely, finer distinctions are recognised among the species concluded to genuinely belong in the genus. Justified records for species retained in the genus are overwhelmingly from fishes of the families Lutjanidae Gill (snappers) and Lethrinidae Bonaparte (emperors), revealing a previously concealed pattern of host-specificity. For H. mutabile, it is argued that only records from western Atlantic lutjanid fishes should be considered genuine; those from plausible Indo-Pacific fishes most likely represent different species. In addition to H. mutabile, eight species are recognised: Hamacreadium cribbi Bray & Justine, 2016, Hamacreadium hainanense Shen, 1990, Hamacreadium interruptum Nagaty, 1941, Hamacreadium lethrini Yamaguti, 1934, Hamacreadium longivesiculum (Yamaguti, 1952) n. comb., Hamacreadium lutiani (Shen, 1990) n. comb., Hamacreadium morgani Baz,1946 and Hamacreadium phyllorchis (Bilqees, 1976) Cribb, 2005. A key to species of Hamacreadium and comprehensive lists of all host-locality records are included.

A complex of species related to Paradiscogaster glebulae (Digenea: Faustulidae) in chaetodontid fishes (Teleostei: Perciformes) of the Great Barrier Reef.

A total of 1523 individuals of 34 species of chaetodontids from the Great Barrier Reef were examined for faustulid trematodes. Specimens resembling Paradiscogaster glebulae Bray, Cribb & Barker, 1994 were found in nine chaetodontid species at three localities. These specimens are shown, on the basis of combined morphological and molecular analyses, to comprise a complex of morphologically similar and partly cryptic species. The complex may comprise as many as six distinct species of which three are resolved here. The true P. glebulae is identified in Chaetodon ornatissimus Cuvier, 1831, Chaetodon aureofasciatus Macleay, 1878, Chaetodon plebeius Cuvier, 1831, Chaetodon rainfordi McCulloch, 1923 and Chaetodon speculum Cuvier, 1831. Two new species are described, Paradiscogaster munozae n. sp. from Heniochus varius (Cuvier, 1829), Heniochus chrysostomus Cuvier, 1831 and Chaetodon citrinellus Cuvier, 1831 and Paradiscogaster melendezi n. sp. from Chaetodon kleinii Bloch, 1790. In terms of morphology the three species differ most clearly in the development of the appendages on the ventral sucker. The three species differ at 3-6consistent bp of ITS2 rDNA. The host-specificity of the three species differs strikingly. P. melendezi n. sp. infects just one fish species, P. glebulae infects species of only one clade of Chaetodon, and P. munozae n. sp. infects quite unrelated species. The basis of this unusual pattern of host-specificity requires further exploration. Two of the species recognised here, P. glebulae and P. munozae n. sp., showed apparent intra-individual variation in the ITS2 rDNA sequences as demonstrated by clear, replicated double peaks in the electropherograms.

Linking demographic processes of juvenile corals to benthic recovery trajectories in two common reef habitats.

Tropical reefs are dynamic ecosystems that host diverse coral assemblages with different life-history strategies. Here, we quantified how juvenile (<50 mm) coral demographics influenced benthic coral structure in reef flat and reef slope habitats on the southern Great Barrier Reef, Australia. Permanent plots and settlement tiles were monitored every six months for three years in each habitat. These environments exhibited profound differences: the reef slope was characterised by 95% less macroalgal cover, and twice the amount of available settlement substrata and rates of coral settlement than the reef flat. Consequently, post-settlement coral survival in the reef slope was substantially higher than that of the reef flat, and resulted in a rapid increase in coral cover from 7 to 31% in 2.5 years. In contrast, coral cover on the reef flat remained low (~10%), whereas macroalgal cover increased from 23 to 45%. A positive stock-recruitment relationship was found in brooding corals in both habitats; however, brooding corals were not directly responsible for the observed changes in coral cover. Rather, the rapid increase on the reef slope resulted from high abundances of broadcast spawning Acropora recruits. Incorporating our results into transition matrix models demonstrated that most corals escape mortality once they exceed 50 mm, but for smaller corals mortality in brooders was double those of spawners (i.e. acroporids and massive corals). For corals on the reef flat, sensitivity analysis demonstrated that growth and mortality of larger juveniles (21-50 mm) highly influenced population dynamics; whereas the recruitment, growth and mortality of smaller corals (<20 mm) had the highest influence on reef slope population dynamics. Our results provide insight into the population dynamics and recovery trajectories in disparate reef habitats, and highlight the importance of acroporid recruitment in driving rapid increases in coral cover following large-scale perturbation in reef slope environments.

Two new species of Phyllodistomum Braun, 1899 (Trematoda: Gorgoderidae Looss, 1899) from Great Barrier Reef fishes.

Two new species of Phyllodistomum Braun, 1899 are described from the urinary bladder of fishes of the Great Barrier Reef. Phyllodistomum hoggettae n. sp. is described from Plectropomus leopardus (leopard coralgrouper) (Serranidae) and P. vaili n. sp. is described from Mulloidichthys vanicolensis (yellowfin goatfish) and M. flavolineatus (yellowstripe goatfish) (Mullidae). These species are compared with 26 previously described marine Phyllodistomum species and found to be distinct in combinations of body shape, sucker ratio and shape of the gonads. Preliminary molecular data also demonstrate that they are distinct from each other and for those other species for which data are available.

Interactions among chronic and acute impacts on coral recruits: the importance of size-escape thresholds.

Newly settled recruits typically suffer high mortality from disturbances, but rapid growth reduces their mortality once size-escape thresholds are attained. Ocean acidification (OA) reduces the growth of recruiting benthic invertebrates, yet no direct effects on survivorship have been demonstrated. We tested whether the reduced growth of coral recruits caused by OA would increase their mortality by prolonging their vulnerability to an acute disturbance: fish herbivory on surrounding algal turf. After two months' growth in ambient or elevated CO2 levels, the linear extension and calcification of coral (Acropora millepora) recruits decreased as CO2 partial pressure (pCO2) increased. When recruits were subjected to incidental fish grazing, their mortality was inversely size dependent. However, we also found an additive effect of pCO2 such that recruit mortality was higher under elevated pCO2 irrespective of size. Compared to ambient conditions, coral recruits needed to double their size at the highest pCO2 to escape incidental grazing mortality. This general trend was observed with three groups of predators (blenny, surgeonfish, and parrotfish), although the magnitude of the fish treatment varied among species. Our study demonstrates the importance of size-escape thresholds in early recruit survival and how OA can shift these thresholds, potentially intensifying population bottlenecks in benthic invertebrate recruitment.

Ocean acidification reduces coral recruitment by disrupting intimate larval-algal settlement interactions.

Ecology Letters (2012) 15: 338-346 ABSTRACT: Successful recruitment in shallow reef ecosystems often involves specific cues that connect planktonic invertebrate larvae with particular crustose coralline algae (CCA) during settlement. While ocean acidification (OA) can reduce larval settlement and the abundance of CCA, the impact of OA on the interactions between planktonic larvae and their preferred settlement substrate are unknown. Here, we demonstrate that CO2 concentrations (800 and 1300 µatm) predicted to occur by the end of this century significantly reduce coral (Acropora millepora) settlement and CCA cover by ≥ 45%. The CCA important for inducing coral settlement (Titanoderma spp., Hydrolithon spp.) were the most deleteriously affected by OA. Surprisingly, the only preferred settlement substrate (Titanoderma) in the experimental controls was avoided by coral larvae as pCO2 increased, and other substrata selected. Our results suggest OA may reduce coral population recovery by reducing coral settlement rates, disrupting larval settlement behaviour, and reducing the availability of the most desirable coralline algal species for successful coral recruitment.

Communication arising. Is coral bleaching really adaptive?

From an experiment in which corals are transplanted between two depths on a Panamanian coral reef, Baker infers that bleaching may sometimes help reef corals to survive environmental change. Although Baker's results hint at further mechanisms by which reef-building corals may acclimatize to changing light conditions, we do not consider that the evidence supports his inference.

Impact of elevated ammonium on reproduction in two Hawaiian scleractinian corals with different life history patterns.

Elevated nutrients have the potential to disrupt reproduction in scleractinian corals, with consequent impacts on population dynamics. Reproduction in broadcast spawning (Montipora capitata) and brooding (Pocillopora damicornis) species was assessed following exposure to elevated ammonium in a microcosm experiment. Planulation in P. damicornis ceased following 4 months of ammonium exposure and did not recover until 3 months after termination of nutrient enrichment. Larval settlement and survivorship were not affected by ammonium enrichment. Few significant changes were found for reproductive parameters of M. capitata. There was a significant but small decrease in egg size (430 microm in control eggs to 408 microm in eggs from ammonium enrichment treatments), but no differences in total fecundity or fertilization success. This may be related to the presence of zooxanthellae in the eggs of M. capitata, in contrast to changes in reproduction previously reported in Acropora species, whose eggs do not contain zooxanthellae.