Phenotypic Selection of Dairy Cattle Infected with Bovine Leukemia Virus Demonstrates Immunogenetic Resilience through NGS-Based Genotyping of BoLA MHC Class II Genes

Characterization of the bovine leukocyte antigen (BoLA) DRB3 gene has shown that specific alleles associate with susceptibility or resilience to the progression of bovine leukemia virus (BLV), measured by proviral load (PVL). Through surveillance of multi-farm BLV eradication field trials, we observed differential phenotypes within seropositive cows that persist from months to years. We sought to develop a multiplex next-generation sequencing workflow (NGS-SBT) capable of genotyping 384 samples per run to assess the relationship between BLV phenotype and two BoLA genes. We utilized longitudinal results from milk ELISA screening and subsequent blood collections on seropositive cows for PVL determination using a novel BLV proviral load multiplex qPCR assay to phenotype the cows. Repeated diagnostic observations defined two distinct phenotypes in our study population, ELISA-positive cows that do not harbor detectable levels of provirus and those who do have persistent proviral loads. In total, 565 cows from nine Midwest dairy farms were selected for NGS-SBT, with 558 cows: 168 BLV susceptible (ELISA-positive/PVL-positive) and 390 BLV resilient (ELISA-positive/PVL-negative) successfully genotyped. Three BoLA-DRB3 alleles, including one novel allele, were shown to associate with disease resilience, *009:02, *044:01, and *048:02 were found at rates of 97.5%, 86.5%, and 90.3%, respectively, within the phenotypically resilient population. Alternatively, DRB3*015:01 and *027:03, both known to associate with disease progression, were found at rates of 81.1% and 92.3%, respectively, within the susceptible population. This study helps solidify the immunogenetic relationship between BoLA-DRB3 alleles and BLV infection status of these two phenotypic groupings of US dairy cattle.

A review of COVID-19 transmission dynamics and clinical outcomes on cruise ships worldwide, January to October 2020

Background Cruise ships provide an ideal setting for transmission of SARS-CoV-2, given the socially dense exposure environment. Aim To provide a comprehensive review of COVID-19 outbreaks on cruise ships. Methods PubMed was searched for COVID-19 cases associated with cruise ships between January and October 2020. A list of cruise ships with COVID-19 was cross-referenced with the United States Centers for Disease Control and Prevention’s list of cruise ships associated with a COVID-19 case within 14 days of disembarkation. News articles were also searched for epidemiological information. Narratives of COVID-19 outbreaks on ships with over 100 cases are presented. Results Seventy-nine ships and 104 unique voyages were associated with COVID-19 cases before 1 October 2020. Nineteen ships had more than one voyage with a case of COVID-19. The median number of cases per ship was three (interquartile range (IQR): 1–17.8), with two notable outliers: the Diamond Princess and the Ruby Princess, which had 712 and 907 cases, respectively. The median attack rate for COVID-19 was 0.2% (IQR: 0.03–1.5), although this distribution was right-skewed with a mean attack rate of 3.7%; 25.9% (27/104) of voyages had at least one COVID-19-associated death. Outbreaks involving only crew occurred later than outbreaks involving guests and crew. Conclusions In the absence of mitigation measures, COVID-19 can spread easily on cruise ships in a susceptible population because of the confined space and high-density contact networks. This environment can create superspreader events and facilitate international spread.

Inherent heterogeneity of influenza A virus stability following aerosolization

Efficient human-to-human transmission represents a necessary adaptation for a zoonotic influenza A virus (IAV) to cause a pandemic. As such, many emerging IAVs are characterized for transmissibility phenotypes in mammalian models, with an emphasis on elucidating viral determinants of transmission and the role host immune responses contribute to mammalian adaptation. Investigations of virus infectivity and stability in aerosols concurrent with transmission assessments have increased in recent years, enhancing our understanding of this dynamic process. Here, we employ a diverse panel of 17 human and zoonotic IAVs, inclusive of seasonally circulating H1N1 and H3N2 viruses, and avian and swine viruses associated with human infection, to evaluate differences in spray factor (a value that assesses efficiency of the aerosolization process), stability, and infectivity following aerosolization. While most seasonal influenza viruses did not exhibit substantial variability within these parameters, there was more heterogeneity among zoonotic influenza viruses, which possess a diverse range of transmission phenotypes. Aging of aerosols at different relative humidities identified strain-specific levels of stability with different profiles identified between zoonotic H3, H5, and H7 subtype viruses associated with human infection. As studies continue to elucidate the complex components governing virus transmissibility, notably aerosol matrices and environmental parameters, considering the relative role of subtype- and strain-specific factors to modulate these parameters will improve our understanding of the pandemic potential of zoonotic influenza A viruses. Importance Transmission of respiratory pathogens through the air can facilitate the rapid and expansive spread of infection and disease through a susceptible population. While seasonal influenza viruses are quite capable of airborne spread, there is a lack of knowledge regarding how well influenza viruses remain viable after aerosolization, and if influenza viruses capable of jumping species barriers to cause human infection differ in this property from seasonal strains. We evaluated a diverse panel of influenza viruses associated with human infection (originating from human, avian, and swine reservoirs) for their ability to remain viable after aerosolization in the laboratory under a range of conditions. We found greater diversity among avian and swine-origin viruses compared with seasonal influenza viruses; strain-specific stability was also noted. Although influenza virus stability in aerosols is an underreported property, if molecular markers associated with enhanced stability are identified, we will be able to quickly recognize emerging strains of influenza that present the greatest pandemic threat.

Does serum Vitamin D affect lipid profile?

Introduction and Aim: Vitamin D, besides its classical physiological functions, exerts effects on brain, prostate, breast, colon, pancreas, and immune cells due to the ubiquitous presence of its receptors. Hypovitaminosis D predisposes individuals to various micro and macro vascular complications of metabolic syndrome and diabetes mellitus. Despite speculations regarding implications of its deficiency on the cardio metabolic health of general/ susceptible population, its role remains underexplored in the Indian population. Materials and Methods: This cross-sectional study carried out in Biochemistry Department of the institution, recruited 219 patients (after obtaining written consent) of both genders above18 years who underwent Vitamin D testing. Blood samples obtained were assayed for HbA1c, C Reactive protein, thiol and lipid. Kruskal Wallis test and Spearman correlation were employed for statistical analysis. Results: Significantly low HDL and high atherogenic index of plasma (AIP) were observed in males with vitamin D deficiency. Significant inverse correlation of vitamin D with CRP and total cholesterol (among vitamin D deficient males) was observed. A significant inverse correlation between serum HDL and AIP and a significant direct correlation between triglyceride and AIP were observed irrespective of their vitamin D status. Heat map showed marginally elevated lipid parameters among vitamin D insufficient males. Conclusion: Vitamin D may emerge as a surrogate marker in risk stratification of patients with diabetes and dyslipidaemia. More insights are required to assess the gender specific susceptibility to dyslipidaemia and atherosclerosis in relation to vitamin D levels.

Mathematical Modelling and Control of COVID-19 Transmission in the Presence of Exposed Immigrants

In this paper, a mathematical model for COVID-19 pandemic that spreads through horizontal transmission in the presence of exposed immigrants is studied. The model has equilibrium points, notably, COVID-19-free equilibrium and COVID-19-endemic equilibrium points. The model exhibits a basic reproduction number, R0 which determines the elimination and persistence of the disease. It was found that when R0 < 1, then the equilibrium becomes locally asymptotically stable and endemic equilibrium does not exists. However, when R0 > 1, the equilibrium is found to be stable globally. This implies that continuous mixing of exposed immigrants with the susceptible population will make the eradication of COVID-19 difficult and endemic in the community. The system is also proved qualitatively to experience transcritical bifurcation close to the COVID-19-free equilibrium at the point R0 = 1. Numerically, the model is used to investigate the impact of certain other relevant parameters on the spread of COVID-19 and how to curtail their effect.

Study of maternal deaths with COVID-19 infection in a tertiary care centre

Background: COVID-19 has been a major speed braker not only for world economy and development but also for health sector. The susceptible population including elderly, co-morbid adults and pregnant females were likewise affected in both major COVID-19 waves in India. Association between COVID-19 cases and pregnancy has been studied throughout the world.COVID-19 is associated with substantial risk of morbidity and mortality in postpartum patients and their infants world-wide, compared with their not-infected pregnant counter-parts, especially if these individuals were symptomatic or have comorbidities.Methods: This single-centre prospective observational study, included all consecutive maternal mortalities with COVID-19 infection admitted to Lokmanya Tilak municipal medical college and general hospital (Mumbai, India), a tertiary referral hospital, from 1 April 2020, to June 2021.In this study, a total of 390 patients were included who were found COVID-19 positive during the study period and 17 patients who died during their admission in hospital. The relation of risk factors and demographics were studied for all the patients.Results: The COVID-19 related maternal mortality was more in women of age group 20-30 years (89%). Most women presented to our centre with complaints of fever, cough, cold or breathlessness (55.5%). Patients who succumbed to COVID-19 were mostly primiparous patients (52.9%) and died within 5 days of delivery (46%). 64% of patients died following 5 days of diagnosis of COVID-19.The co-morbidity present in most patients with COVID-19 associated maternal mortality was pre-eclampsia (31.5%). Most patients were referred with only 17% patients registered at our centre and the type of delay involved in management was mostly Type 1 and 2 (82.2%)Conclusions: Multi-centre retrospective analysis with larger population size is required in order for this to be statistically significant.

Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive population turnover, is not thoroughly understood. We conducted a large-scale phylodynamic analysis of 27 human pathogenic RNA viruses spanning diverse life history traits in search of unifying trends that shape virus evolution. For most virus species, we identify multiple, co-circulating lineages with low turnover rates. These lineages appear to be largely noncompeting and likely occupy semi-independent epidemiological niches that are not regionally or seasonally defined. Typically, intra-lineage mutational signatures are similar to inter-lineage signatures. The principal exception are members of the family Picornaviridae, for which mutations in capsid protein genes are primarily lineage-defining. The persistence of virus lineages appears to stem from limited outbreaks within small communities so that only a minor fraction of the global susceptible population is infected at any time. As disparate communities become increasingly connected through globalization, interaction and competition between lineages might increase as well, which could result in changing selective pressures and increased diversification and/or pathogenicity. Thus, in addition to zoonotic events, ongoing surveillance of familiar, endemic viruses appears to merit global attention with respect to the prevention or mitigation of future pandemics.SignificanceNumerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential of causing new pandemics? We show that most human pathogenic RNA viruses form multiple, co-circulating lineages with low turnover rates. These lineages appear to be largely noncompeting and occupy distinct epidemiological niches that are not regionally or seasonally defined, and their persistence appears to stem from limited outbreaks in small communities so that a minor fraction of the global susceptible population is infected at any time. However, due to globalization, interaction and competition between lineages might increase, potentially leading to increased diversification and pathogenicity. Thus, endemic viruses appear to merit global attention with respect to the prevention of future pandemics.

Transcriptomic analysis of resistance and short-term induction response to pyrethroids, in Anopheles coluzzii legs

Background Insecticide-treated bed nets and indoor residual spraying comprise the major control measures against Anopheles gambiae sl, the dominant vector in sub-Saharan Africa. The primary site of contact with insecticide is through the mosquitoes’ legs, which represents the first barrier insecticides have to bypass to reach their neuronal targets. Proteomic changes and leg cuticle modifications have been associated with insecticide resistance that may reduce the rate of penetration of insecticides. Here, we performed a multiple transcriptomic analyses focusing on An. coluzzii legs. Results Firstly, leg-specific enrichment analysis identified 359 genes including the pyrethroid-binder SAP2 and 2 other chemosensory proteins, along with 4 ABCG transporters previously shown to be leg enriched. Enrichment of gene families included those involved in detecting chemical stimuli, including gustatory and ionotropic receptors and genes implicated in hydrocarbon-synthesis. Subsequently, we compared transcript expression in the legs of a highly resistant strain (VK7-HR) to both a strain with very similar genetic background which has reverted to susceptibility after several generations without insecticide pressure (VK7-LR) and a lab susceptible population (NG). Two hundred thirty-two differentially expressed genes (73 up-regulated and 159 down-regulated) were identified in the resistant strain when compared to the two susceptible counterparts, indicating an over-expression of phase I detoxification enzymes and cuticular proteins, with decrease in hormone-related metabolic processes in legs from the insecticide resistant population. Finally, we analysed the short-term effect of pyrethroid exposure on An. coluzzii legs, comparing legs of 1 h-deltamethrin-exposed An. coluzzii (VK7-IN) to those of unexposed mosquitoes (VK7-HR) and identified 348 up-regulated genes including those encoding for GPCRs, ABC transporters, odorant-binding proteins and members of the divergent salivary gland protein family. Conclusions The data on An. coluzzii leg-specific transcriptome provides valuable insights into the first line of defense in pyrethroid resistant and short-term deltamethrin-exposed mosquitoes. Our results suggest that xenobiotic detoxification is likely occurring in legs, while the enrichment of sensory proteins, ABCG transporters and cuticular genes is also evident. Constitutive resistance is primarily associated with elevated levels of detoxification and cuticular genes, while short-term insecticide-induced tolerance is linked with overexpression of transporters, GPCRs and GPCR-related genes, sensory/binding and salivary gland proteins.

A wind speed threshold for increased outdoor transmission of coronavirus: an ecological study

Background To examine whether outdoor transmission may contribute to the COVID-19 epidemic, we hypothesized that slower outdoor wind speed is associated with increased risk of transmission when individuals socialize outside. Methods Daily COVID-19 incidence reported in Suffolk County, NY, between March 16th and December 31st, 2020, was the outcome. Average wind speed and maximal daily temperature were collated by the National Oceanic and Atmospheric Administration. Negative binomial regression was used to model incidence rates while adjusting for susceptible population size. Results Cases were very high in the initial wave but diminished once lockdown procedures were enacted. Most days between May 1st, 2020, and October 24th, 2020, had temperatures 16–28 °C and wind speed diminished slowly over the year and began to increase again in December 2020. Unadjusted and multivariable-adjusted analyses revealed that days with temperatures ranging between 16 and 28 °C where wind speed was < 8.85 km per hour (KPH) had increased COVID-19 incidence (aIRR = 1.45, 95% C.I. = [1.28–1.64], P < 0.001) as compared to days with average wind speed ≥ 8.85 KPH. Conclusion Throughout the U.S. epidemic, the role of outdoor shared spaces such as parks and beaches has been a topic of considerable interest. This study suggests that outdoor transmission of COVID-19 may occur by noting that the risk of transmission of COVID-19 in the summer was higher on days with low wind speed. Outdoor use of increased physical distance between individuals, improved air circulation, and use of masks may be helpful in some outdoor environments where airflow is limited.

Assessing the Impact of (Self)-Quarantine through a Basic Model of Infectious Disease Dynamics

We introduce a system of differential equations to assess the impact of (self-)quarantine of symptomatic infectious individuals on disease dynamics. To this end we depart from using the classic bilinear infection process, but remain within the framework of the mass-action assumption. From the mathematical point of view, the model we propose is interesting due to the lack of continuous differentiability at disease-free steady states, which implies that the basic reproductive number cannot be computed following established mathematical approaches for certain parameter values. However, we parametrise our mathematical model using published values from the COVID-19 literature, and analyse the model simulations. We also contrast model simulations against publicly available COVID-19 test data, focusing on the first wave of the pandemic during March–July 2020 in the UK. Our simulations indicate that actual peak case numbers might have been as much as 200 times higher than the reported positive test cases during the first wave in the UK. We find that very strong adherence to self-quarantine rules yields (only) a reduction of 22% of peak numbers and delays the onset of the peak by approximately 30–35 days. However, during the early phase of the outbreak, the impact of (self)-quarantine is much more significant. We also take into account the effect of a national lockdown in a simplistic way by reducing the effective susceptible population size. We find that, in case of a 90% reduction of the effective susceptible population size, strong adherence to self-quarantine still only yields a 25% reduction of peak infectious numbers when compared to low adherence. This is due to the significant number of asymptomatic infectious individuals in the population.