A non-enzymatic test for SARS-CoV-2 RNA using DNA nanoswitches.

The emergence of a highly contagious novel coronavirus in 2019 led to an unprecedented need for large scale diagnostic testing. The associated challenges including reagent shortages, cost, deployment delays, and turnaround time have all highlighted the need for an alternative suite of low-cost tests. Here, we demonstrate a diagnostic test for SARS-CoV-2 RNA that provides direct detection of viral RNA and eliminates the need for costly enzymes. We employ DNA nanoswitches that respond to segments of the viral RNA by a change in shape that is readable by gel electrophoresis. A new multi-targeting approach samples 120 different viral regions to improve the limit of detection and provide robust detection of viral variants. We apply our approach to a cohort of clinical samples, positively identifying a subset of samples with high viral loads. Since our method directly detects multiple regions of viral RNA without amplification, it eliminates the risk of amplicon contamination and renders the method less susceptible to false positives. This new tool can benefit the COVID-19 pandemic and future emerging outbreaks, providing a third option between amplification-based RNA detection and protein antigen detection. Ultimately, we believe this tool can be adapted both for low-resource onsite testing as well as for monitoring viral loads in recovering patients.

Associations of Anaplasma phagocytophilum Bacteria Variants in Ixodes scapularis Ticks and Humans, New York, USA.

Anaplasmosis, caused by the tickborne bacterium Anaplasma phagocytophilum, is an emerging public health threat in the United States. In the northeastern United States, the blacklegged tick (Ixodes scapularis) transmits the human pathogenic genetic variant of A. phagocytophilum (Ap-ha) and a nonpathogenic variant (Ap-V1). New York has recently experienced a rapid and geographically focused increase in cases of anaplasmosis. We analyzed A. phagocytophilum-infected I. scapularis ticks collected across New York during 2008-2020 to differentiate between variants and calculate an entomological risk index (ERI) for each. Ap-ha ERI varied between regions and increased in all regions during the final years of the study. Space-time scan analyses detected expanding clusters of Ap-ha located within documented anaplasmosis hotspots. Ap-ha ERI was more positively correlated with anaplasmosis incidence than non-genotyped A. phagocytophilum ERI. Our findings help elucidate the relationship between the spatial ecology of A. phagocytophilum variants and anaplasmosis.

SARS-CoV-2 Vaccine Breakthrough by Omicron and Delta Variants, New York, USA.

Recently emerged SARS-CoV-2 variants have greater potential than earlier variants to cause vaccine breakthrough infections. During emergence of the Delta and Omicron variants, a matched case-control analysis used a viral genomic sequence dataset linked with demographic and vaccination information from New York, USA, to examine associations between virus lineage and patient vaccination status, patient age, vaccine type, and time since vaccination. Case-patients were persons infected with the emerging virus lineage, and controls were persons infected with any other virus lineage. Infections in fully vaccinated and boosted persons were significantly associated with the Omicron lineage. Odds of infection with Omicron relative to Delta generally decreased with increasing patient age. A similar pattern was observed with vaccination status during Delta emergence but was not significant. Vaccines offered less protection against Omicron, thereby increasing the number of potential hosts for emerging variants.

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.

SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In this study, we compare the dynamics of two variants, Alpha and Iota, by integrating genomic surveillance data to estimate the effective reproduction number (Rt) of the variants. We use Connecticut, United States, in which Alpha and Iota co-circulated in 2021. We find that the Rt of these variants were up to 50% larger than that of other variants. We then use phylogeography to show that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of Alpha were larger than those resulting from Iota introductions. By monitoring the dynamics of individual variants throughout our study period, we demonstrate the importance of routine surveillance in the response to COVID-19.

Burden and severity of disease of aromatic L-amino acid decarboxylase deficiency: a systematic literature review.

OBJECTIVE: The objective was to investigate the severity of aromatic L-amino acid decarboxylase deficiency (AADCd) as reported in the published literature and to collate evidence of the clinical manifestations of AADCd, and the impact of the disease on patients, caregivers, and healthcare systems. METHODS: Published articles reporting severity of disease or disease impact were eligible for inclusion in this review. Articles were searched in MEDLINE, EMBASE, Cochrane CENTRAL, TRIP medical, and CRD databases in October 2021. The quality of the included studies was investigated using a modified version of the grading system of the Centre for Evidence-Based Medicine (CEBM). Descriptive data of the literature was extracted and a narrative synthesis of the results across studies was conducted. This review is reported according to the PRISMA reporting guidelines for systematic reviews. RESULTS: The search identified 970 unique reports, of which 59 met eligibility criteria to be included in the review. Of these, 48 included reports provided details on the clinical manifestations of AADCd. Two reports explored the disease impact on patients, while four described the impact on caregivers. Five reports assessed the impact on healthcare systems. Individuals with AADCd experience very severe clinical manifestations regardless of motor milestones achieved, and present with a spectrum of other complications. Individuals with AADCd present with very limited function, which, in combination with additional complications, substantially impact the quality-of-life of individuals and their caregivers. The five studies which explore the impact on the healthcare system reported that adequate care of individuals with AADCd requires a vast array of medical services and supportive therapies. CONCLUSIONS: Irrespective of the ambulatory status of individuals, AADCd is a debilitating disease that significantly impacts quality-of-life for individuals and caregivers. It impacts the healthcare system due to the need for complex coordinated activities of a multidisciplinary specialist team.

Spatiotemporal Analyses of 2 Co-Circulating SARS-CoV-2 Variants, New York State, USA.

The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in late 2020 and early 2021 raised alarm worldwide because of their potential for increased transmissibility and immune evasion. Elucidating the evolutionary and epidemiologic dynamics among novel SARS-CoV-2 variants is essential for understanding the trajectory of the coronavirus disease pandemic. We describe the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) variants in New York State, USA, during December 2020-April 2021 through phylogeographic analyses, space-time scan statistics, and cartographic visualization. Our results indicate that B.1.526 probably evolved in New York City, where it was displaced as the dominant lineage by B.1.1.7 months after its initial appearance. In contrast, B.1.1.7 became dominant earlier in regions with fewer B.1.526 infections. These results suggest that B.1.526 might have delayed the initial spread of B.1.1.7 in New York City. Our combined spatiotemporal methodologies can help disentangle the complexities of shifting SARS-CoV-2 variant landscapes.

Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA.

Of 379 severe acute respiratory syndrome coronavirus 2 samples collected in New York, USA, we detected 86 Omicron variant sequences containing Delta variant mutation P681R. Probable explanations were co-infection with 2 viruses or contamination/amplification artifact. Repeated library preparation with fewer cycles showed the P681R calls were artifactual. Unusual mutations should be interpreted with caution.

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages.

Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this assessment requires that a true comparison can be made between the new variant and its predecessors because factors other than the virus genotype may influence spread and transmission. In this study, we develop a framework that integrates genomic surveillance data to estimate the relative effective reproduction number (R t ) of co-circulating lineages. We use Connecticut, a state in the northeastern United States in which the SARS-CoV-2 variants B.1.1.7 and B.1.526 co-circulated in early 2021, as a case study for implementing this framework. We find that the R t of B.1.1.7 was 6-10% larger than that of B.1.526 in Connecticut in the midst of a COVID-19 vaccination campaign. To assess the generalizability of this framework, we apply it to genomic surveillance data from New York City and observe the same trend. Finally, we use discrete phylogeography to demonstrate that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of B.1.1.7 were larger than those resulting from B.1.526 introductions. Our framework, which uses open-source methods requiring minimal computational resources, may be used to monitor near real-time variant dynamics in a myriad of settings.

Epidemiology and Spatial Emergence of Anaplasmosis, New York, USA, 2010‒2018.

Human granulocytic anaplasmosis, a tickborne disease caused by the bacterium Anaplasma phagocytophilum, was first identified during 1994 and is now an emerging public health threat in the United States. New York state (NYS) has experienced a recent increase in the incidence of anaplasmosis. We analyzed human case surveillance and tick surveillance data collected by the NYS Department of Health for spatiotemporal patterns of disease emergence. We describe the epidemiology and growing incidence of anaplasmosis cases reported during 2010-2018. Spatial analysis showed an expanding hot spot of anaplasmosis in the Capital Region, where incidence increased >8-fold. The prevalence of A. phagocytophilum increased greatly within tick populations in the Capital Region over the same period, and entomologic risk factors were correlated with disease incidence at a local level. These results indicate that anaplasmosis is rapidly emerging in a geographically focused area of NYS, likely driven by localized changes in exposure risk.

A Comparative Spatial and Climate Analysis of Human Granulocytic Anaplasmosis and Human Babesiosis in New York State (2013-2018).

Human granulocytic anaplasmosis (HGA) and human babesiosis are tick-borne diseases spread by the blacklegged tick (Ixodes scapularis Say, Acari: Ixodidae) and are the result of infection with Anaplasma phagocytophilum and Babesia microti, respectively. In New York State (NYS), incidence rates of these diseases increased concordantly until around 2013, when rates of HGA began to increase more rapidly than human babesiosis, and the spatial extent of the diseases diverged. Surveillance data of tick-borne pathogens (2007 to 2018) and reported human cases of HGA (n = 4,297) and human babesiosis (n = 2,986) (2013-2018) from the New York State Department of Health (NYSDOH) showed a positive association between the presence/temporal emergence of each pathogen and rates of disease in surrounding areas. Incidence rates of HGA were higher than human babesiosis among White and non-Hispanic/non-Latino individuals, as well as all age and sex groups. Human babesiosis exhibited higher rates among non-White individuals. Climate, weather, and landscape data were used to build a spatially weighted zero-inflated negative binomial (ZINB) model to examine and compare associations between the environment and rates of HGA and human babesiosis. HGA and human babesiosis ZINB models indicated similar associations with forest cover, forest land cover change, and winter minimum temperature; and differing associations with elevation, urban land cover change, and winter precipitation. These results indicate that tick-borne disease ecology varies between pathogens spread by I. scapularis.

Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States.

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2,500 COVID-19 cases associated with this variant have been detected in the United States (US) since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight that the primary ports of entry for B.1.1.7 in the US were in New York, California, and Florida. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid- to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States.

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

Serologic Survey of Mosquito-Borne Viruses in Hunter-Harvested White-Tailed Deer (Odocoileus virginianus), New York State.

Sera from white-tailed deer (WTD, Odocoileus virginianus) hunter-harvested throughout New York State (NYS), 2007-2015, were tested by plaque reduction neutralization for antibodies against nine mosquito-borne viruses from the families Peribunyaviridae, Flaviviridae, and Togaviridae. Overall, 76.1% (373/490) of sampled WTD were seropositive against at least one virus, and 38.8% were exposed to multiple viruses. The seropositivity rate in adult WTD (78.0%) was significantly greater (P < 0.0001) than that in fawns (47.7%). Neutralizing antibodies against California serogroup viruses were most common in WTD sampled across all regions (67.1%), followed by the Bunyamwera serogroup (BUN) (37.6%). Jamestown Canyon and Cache Valley orthobunyaviruses were responsible for most California and BUN infections, respectively. Seroprevalence rates to West Nile virus were higher in samples originating from Long Island (LI) (19.0%) than in those originating from the central (7.3%), western (5.0%), and Hudson Valley (4.4%) regions of NYS. Antibodies to Eastern equine encephalitis virus were seen primarily in WTD from central NYS (5.1%), where annual enzootic activity occurs, but low rates were documented in western NYS (1.4%) and LI (1.7%). Low rates of Potosi and LaCrosse orthobunyavirus, and Highlands J virus antibodies were detected over the course of this investigation. St. Louis encephalitis virus (or a closely related virus) antibodies were detected in samples collected from central and western NYS, suggesting local virus transmission despite a lack of evidence from routine mosquito surveillance. Serologic results demonstrate the value of WTD in NYS as an indicator of arbovirus distribution and recent transmission on a relatively fine spatial scale.

Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis.

Outbreaks of cyclosporiasis, a food-borne illness caused by the coccidian parasite Cyclospora cayetanensis have increased in the USA in recent years, with approximately 2300 laboratory-confirmed cases reported in 2018. Genotyping tools are needed to inform epidemiological investigations, yet genotyping Cyclospora has proven challenging due to its sexual reproductive cycle which produces complex infections characterized by high genetic heterogeneity. We used targeted amplicon deep sequencing and a recently described ensemble-based distance statistic that accommodates heterogeneous (mixed) genotypes and specimens with partial genotyping data, to genotype and cluster 648 C. cayetanensis samples submitted to CDC in 2018. The performance of the ensemble was assessed by comparing ensemble-identified genetic clusters to analogous clusters identified independently based on common food exposures. Using these epidemiologic clusters as a gold standard, the ensemble facilitated genetic clustering with 93.8% sensitivity and 99.7% specificity. Hence, we anticipate that this procedure will greatly complement epidemiologic investigations of cyclosporiasis.

Influence of PapMV nanoparticles on the kinetics of the antibody response to flu vaccine.

BACKGROUND: The addition of an adjuvant to a vaccine is a promising approach to increasing strength and immunogenicity towards antigens. Despite the fact that adjuvants have been used in vaccines for decades, their mechanisms of action and their influence on the kinetics of the immune response are still not very well understood. The use of papaya mosaic virus (PapMV) nanoparticles-a novel TLR7 agonist-was recently shown to improve and broaden the immune response directed to trivalent inactivated flu vaccine (TIV) in mice and ferrets. RESULTS: We investigated the capacity of PapMV nanoparticles to increase the speed of the immune response toward TIV. PapMV nanoparticles induced a faster and stronger humoral response to TIV that was measured as early as 5 days post-immunization. The addition of PapMV nanoparticles was shown to speed up the differentiation of B-cells into early plasma cells, and increased the growth of germinal centers in a CD4+ dependent manner. TIV vaccination with PapMV nanoparticles as an adjuvant protected mice against a lethal infection as early as 10 days post-immunization. CONCLUSION: In conclusion, PapMV nanoparticles are able to accelerate a broad humoral response to TIV. This property is of the utmost importance in the field of vaccination, especially in the case of pandemics, where populations need to be protected as soon as possible after vaccination.

PapMV nanoparticles improve mucosal immune responses to the trivalent inactivated flu vaccine.

BACKGROUND: Trivalent inactivated flu vaccines (TIV) are currently the best means to prevent influenza infections. However, the protection provided by TIV is partial (about 50%) and it is needed to improve the efficacy of protection. Since the respiratory tract is the main site of influenza replications, a vaccine that triggers mucosal immunity in this region can potentially improve protection against this disease. Recently, PapMV nanoparticles used as an adjuvant in a formulation with TIV administered by the subcutaneous route have shown improving the immune response directed to the TIV and protection against an influenza challenge. FINDINGS: In the present study, we showed that intranasal instillation with a formulation containing TIV and PapMV nanoparticles significantly increase the amount of IgG, IgG2a and IgA in lungs of vaccinated mice as compared to mice that received TIV only. Instillation with the adjuvanted formulation leads to a more robust protection against an influenza infection with a strain that is lethal to mice vaccinated with the TIV. CONCLUSIONS: We demonstrate for the first time that PapMV nanoparticles are an effective and potent mucosal adjuvant for vaccination.

Calling by concluding sentinels: coordinating cooperation or revealing risk?

Efficient cooperation requires effective coordination of individual contributions to the cooperative behaviour. Most social birds and mammals involved in cooperation produce a range of vocalisations, which may be important in regulating both individual contributions and the combined group effort. Here we investigate the role of a specific call in regulating cooperative sentinel behaviour in pied babblers (Turdoides bicolor). 'Fast-rate chuck' calls are often given by sentinels as they finish guard bouts and may potentially coordinate the rotation of individuals as sentinels, minimising time without a sentinel, or may signal the presence or absence of predators, regulating the onset of the subsequent sentinel bout. We ask (i) when fast-rate chuck calls are given and (ii) what effect they have on the interval between sentinel bouts. Contrary to expectation, we find little evidence that these calls are involved in regulating the pied babbler sentinel system: observations revealed that their utterance is influenced only marginally by wind conditions and not at all by habitat, while observations and experimental playback showed that the giving of these calls has no effect on inter-bout interval. We conclude that pied babblers do not seem to call at the end of a sentinel bout to maximise the efficiency of this cooperative act, but may use vocalisations at this stage to influence more individually driven behaviours.