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.

Immunity acquired by a minority active fraction of the population could explain COVID-19 spread in Greater Buenos Aires (June-November 2020)

The COVID-19 pandemic had an uneven development in different countries. In Argentina, the pandemic began in march 2020 and, during the first 3 months, the vast majority of cases were concentrated in a densely populated region that includes the city of Buenos Aires (country capital) and the Greater Buenos Aires area that surrounds it. This work focuses on the spread of COVID-19 between June and November 2020 in Greater Buenos Aires. Within this period of time there was no vaccine, basically only the early wild strain of SARS-CoV-2 was present, and the official restriction and distancing measures in this region remained more or less constant. Under these particular conditions, the incidences show a sharp rise from June 2020 and begin to decrease towards the end of August until the end of November 2020. In this work we study, through mathematical modelling and available epidemiological information, the spread of COVID-19 in this region and period of time. We show that a coherent explanation of the evolution of incidences can be obtained assuming that only a minority fraction of the population got involved in the spread process, so that the incidences decreased as this group of people was becoming immune. The observed evolution of the incidences could then be a consequence at the population level of lasting immunity conferred by SARS-CoV-2.

Analysis of chronic diseases associated to SARS-CoV-2 infection in children and young people in Mexico

<p>The emergence of COVID-19, a disease caused by SARS-CoV-2, was first reported in December 2019. It then spread in pandemic proportions, creating a human health emergency that was declared a pandemic by the World Health Organization. The airborne transmission of the SARS-CoV-2 virus, mainly through droplets of saliva, has been highly effective, depending on the viral variant. The present study provides clinical-epidemiological information on the general population without discriminating by socioeconomic and occupational factors. A total of 8507 positive cases, with 408384 official metadata, were analyzed. These cases correspond to the exponential phase of the first epidemic wave (March-June 2020) in Mexico. The cohort consisted of children and young people up to 20 years of age. The putative risk factors for SARS-CoV-2 infection due to chronic diseases were also analyzed. In this cohort, the frequency of SARS-CoV-2 infection was 3%, with a 9% rate of active infections and a mortality rate of 1%. The greatest association was between COVID-19 and metabolic diseases, with 31%. This is the first study that analyzed the health conditions associated with COVID-19 infection in children and young people in Mexico during the first SARS-CoV-2 epidemic wave, in the absence of acquired or induced immunity factors. The results, although preliminary, may contribute to the management of COVID-19 patients during the prevention and hospitalization stages. Given the sustained expansion of the epidemic and the greater availability of data, it would be useful to make an integrative analysis of the rural population, which has remained active in the labor market given that agriculture is considered an essential activity.</p>

Plague – ”The Turkish disease”: a traditional Romanian perception (historical, theological, ethnological and epidemiological aspects)

The article addresses the issue of the traditional Romanian perception of the plague as ”Turkish disease” and presents relevant historical, theological, ethnological and epidemiological information. This perception is based on the memory of the frequent wars waged by the Ottomans on Romanian territory; wars during which contagious diseases were recurrent, and implicitly the plague. In historiography, the invocation of the plague epidemics in the context of Ottoman history was nuanced in the works of Mihail Critobul from Imbros, Dimitrie Cantemir, Montesquieu, Constantin Bazili. The reluctance of the natives towards the Turks is explained by the cultural, religious and linguistic differences, by the behavior of the Ottomans and by the non-acceptance of the other’s values. The inhabitants of the principalities believed that the plague also entered through the Ottoman ships coming from Constantinople and moored in the ports of Galați and Brăila. The epidemiological phobias of the natives were amplified by the fact that the Turks, especially those from the royal family, neglected any sanitary restrictions during the plague epidemics. The Ottoman plague’s fatalism is explained by their religious beliefs. The divine factor is also invoked in Romanian folklore, the plague being perceived as God’s punishment sent to the Turks for the misfortunes brought to the Romanians.

Identification of risk factors associated with national transmission and late presentation of HIV-1, Denmark, 2009 to 2017

Background Despite availability of pre-exposure prophylaxis (PrEP), the incidence of HIV-1 in Europe remained stable the past decade. Reduction of new HIV-1 infections requires more knowledge about the profiles of high-risk transmitters and late presenters (LP). Aim We aimed to investigate risk factors associated with HIV-1 transmission clusters and late presentation with HIV-1 in Denmark. Methods Blood samples and epidemiological information were collected from newly diagnosed HIV-1 patients between 2009 and 2017. We genotyped pol genes and performed phylogenetic analyses to identify clusters. Risk factors for clustering and LP were investigated with partial proportional odds and logistic regression. Covariates included transmission mode, HIV-1 subtype, age, origin and cluster activity. Results We included 1,040 individuals in the analysis, 59.6% identified with subtype B and 48.4% in a cluster. Risk factors for clustering included Danish origin (odds ratio (OR): 2.95; 95% confidence interval (CI): 2.21–3.96), non-LP (OR: 1.44; 95% CI: 1.12–1.86), and men who have sex with men (MSM). Increasing age and non-B subtype infection decreased risk (OR: 0.69; 95% CI: 0.50–0.94). Risk for late presentation was lower for active clusters (OR: 0.60; 95% CI: 0.44–0.82) and Danish origin (OR: 0.43; 95% CI: 0.27–0.67). Non-Danish MSM had a lower risk than non-Danish heterosexuals (OR: 0.34; 95% CI: 0.21–0.55). Conclusion HIV-1 transmission in Denmark is driven by early diagnosed, young, subtype B infected MSM. These may benefit most from PrEP. Non-Danish heterosexual HIV-1 patients could benefit from improved communication to achieve earlier diagnosis and treatment.

Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and humans on farms. High number of farm infections (68/126) in minks and farm workers (>50% of farms) were detected, with limited community spread. Three of five initial introductions of SARS-CoV-2 led to subsequent spread between mink farms until November 2020. Viruses belonging to the largest cluster acquired an amino acid substitution in the receptor binding domain of the Spike protein (position 486), evolved faster and spread longer and more widely. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combining genetic information with epidemiological information when investigating outbreaks at the animal-human interface.

Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

Porcine circovirus-like virus (PCLV) is a type of circular Rep-encoding single-stranded DNA virus and may be associated with the development of diarrheal symptoms in pigs. In this study, we retrospectively analyzed three years of past cases in Anhui, China, and reported a case of hemorrhagic enteritis and death in a pregnant sow possibly caused by PCLV. In addition, we analyzed the evolutionary characteristics of PCLV and found that mutation, recombination and selective pressure all played an important role in the evolution of PCLV. We identified N15D and T17S as well as L56T, T58R, K59Q, M62R, L75I and R190K mutations in two different branches, and we noted recombination events in the Rep of a group of Chinese strains. Analysis of selection pressure revealed that PCLV gained more positive selection, indicating that the virus is in a continuous evolutionary state. The PR2 plot, ENC-plot and neutrality analysis showed a greater role of natural selection than that of mutational pressure in the formation of codon usage patterns. This study is the first to identify PCLV in sows with hemorrhagic dysentery and death, and it provides new epidemiological information on PCLV infection in pigs in China.

Extensive Genome Exploration of Clostridium botulinum Group III Field Strains

In animals, botulism is commonly sustained by botulinum neurotoxin C, D or their mosaic variants, which are produced by anaerobic bacteria included in Clostridium botulinum group III. In this study, a WGS has been applied to a large collection of C. botulinum group III field strains in order to expand the knowledge on these BoNT-producing Clostridia and to evaluate the potentiality of this method for epidemiological investigations. Sixty field strains were submitted to WGS, and the results were analyzed with respect to epidemiological information and compared to published sequences. The strains were isolated from biological or environmental samples collected in animal botulism outbreaks which occurred in Italy from 2007 to 2016. The new sequenced strains belonged to subspecific groups, some of which were already defined, while others were newly characterized, peculiar to Italian strains and contained genomic features not yet observed. This included, in particular, two new flicC types (VI and VII) and new plasmids which widen the known plasmidome of the species. The extensive genome exploration shown in this study improves the C. botulinum and related species classification scheme, enriching it with new strains of rare genotypes and permitting the highest grade of discrimination among strains for forensic and epidemiological applications.

Multi-Model Selection and Analysis for COVID-19

In the face of an increasing number of COVID-19 infections, one of the most crucial and challenging problems is to pick out the most reasonable and reliable models. Based on the COVID-19 data of four typical cities/provinces in China, integer-order and fractional SIR, SEIR, SEIR-Q, SEIR-QD, and SEIR-AHQ models are systematically analyzed by the AICc, BIC, RMSE, and R means. Through extensive simulation and comprehensive comparison, we show that the fractional models perform much better than the corresponding integer-order models in representing the epidemiological information contained in the real data. It is further revealed that the inflection point plays a vital role in the prediction. Moreover, the basic reproduction numbers R0 of all models are highly dependent on the contact rate.

Epidemiology of Treated Epilepsy in New Zealand Children: A Focus on Ethnicity

Objective:To determine the period prevalence and incidence of treated epilepsy in a New Zealand (NZ) pediatric cohort with a focus on ethnicity and socioeconomic status.Methods:This was a retrospective cohort study. The NZ Pharmaceutical Collection database was searched for individuals (≤18 years) dispensed an antiseizure medication (ASM) in 2015 from areas capturing 48% of the NZ pediatric population. Medical records of identified cases were reviewed to ascertain the indication for the ASM prescription. Population data was derived from the NZ 2013 Census.Results:3557 ASMs were prescribed during 2015 in 2594 children, of whom 1717 (66%) children had epilepsy. An indication for prescription was ascertained for 3332/3557 (94%) of ASMs. The period prevalence of treated epilepsy was 3.4 per 1000 children. Children in the most deprived areas had 1.9 times the rate of treated epilepsy (95% CI 1.6-2.2) than those from the least deprived areas. Prevalence was similar for most ethnic groups (European/Other - 3.7, 95% CI 3.4-3.9; Pacific Peoples - 3.6, 95% CI 3.2-4.1; Māori - 3.4, 95% CI 3.1-3.8) apart from Asians, who had a lower prevalence of 2.3 per 1000 (95% CI 2.0-2.6). However, when adjusted for socioeconomic deprivation, the prevalence of epilepsy was highest in Europeans and similar in Māori, Pacific and Asian children.Conclusions:This is the largest pediatric epidemiology epilepsy study where diagnosis of epilepsy was confirmed by case review. This is the first study to provide epidemiological information for pediatric epilepsy in Māori and Pacific children.