Seropositivity and flight-associated risk factors for SARS-CoV-2 infection among asylum seekers arriving in Berlin, Germany – a cross-sectional study

Introduction: Refugees and asylum seekers might be at increased risk of SARS-CoV-2 infection due to precarious living conditions during flight. Methods: Between March 24th and June 15th 2021, we conducted a cross-sectional study among adult asylum seekers arriving in Berlin. Each participant was tested for acute SARS-CoV-2 infection with a nasopharyngeal swab using reverse transcriptase PCR (rt-PCR), and for anti-SARS-CoV-2-S1 IgG antibodies using ELISA. Seropositivity, antibody avidity, and data on flight history were used to categorize individuals into two groups according to the estimated time of infection before or during flight. Sociodemographic characteristics, COVID-19 related symptoms, hygiene behaviors, and living conditions during transit were assessed using two self-report questionnaires. Results: Among 1041 participants (34·5% female, mean age 32·6 years), most frequently reported countries of origin were Moldova (20·5%), Georgia (18·9%), Syria (13·0%), Afghanistan (11·3%), and Vietnam (9·1%). Seropositivity rate was 25·1% and incidence rate of acute SARS-CoV-2 infection was 2·8%. A higher likelihood for seropositivity was observed in women (OR [95%CI]=1·64 [1·05-2·57]) but reduced by frequent hygiene behaviors (OR [95%CI]=0·75 [0·59-0·96]) or traveling by plane (OR [95%CI]=0·58 [0·35-0·96]). Other associated factors were lower educational level, accommodation in refugee shelters, traveling with children or by foot, and COVID-19 information seeking. Conclusion: Flight-associated risk factors such as accommodation in a refugee shelter and poor hygiene behaviors are associated with an elevated risk of infection, which should be addressed by public health interventions. Clinical trial registration: [https://doi.org/10.1186/ISRCTN17401860], identifier [17401860]

Monkeypox in-patients with severe anal pain

Berlin is amongst the cities most affected by the current monkeypox outbreak. Here, we report clinical characteristics of the first patients with confirmed monkeypox admitted to our center. We analyzed anamnestic, clinical, and laboratory data. Within a period of 2 weeks, six patients were hospitalized in our unit. All were MSM and had practiced condomless receptive anal intercourse in the weeks preceding admission. The chief complaint in all patients but one was severe anal pain unprecedented in severity. Investigations revealed proctitis, as well as anal and rectal ulcers with detection of monkeypox virus. Our findings support the hypothesis that sexual transmission plays a role in the current outbreak

Rabies virus in slaughtered dogs for meat consumption in Ghana: A potential risk for rabies transmission

Dog-mediated rabies is responsible for approximately 60,000 human deaths annually worldwide. Although dog slaughter for human consumption and its potential risk for rabies transmission has been reported, mainly in some parts of Western Africa and South-East Asia, more information on this and factors that influence dog meat consumption is required for a better understanding from places like Ghana where the practice is common. We tested 144 brain tissues from apparently healthy dogs slaughtered for human consumption for the presence of rabies viruses using a Lyssavirus-specific real-Time RT-PCR. Positive samples were confirmed by virus genome sequencing. We also administered questionnaires to 541 dog owners from three regions in Ghana and evaluated factors that could influence dog meat consumption. We interacted with butchers and observed slaughtering and meat preparation procedures. Three out of 144 (2.1%) brain tissues from apparently healthy dogs tested positive for rabies virus RNA. Two of the viruses with complete genomes were distinct from one another, but both belonged to the Africa 2 lineage. The third virus with a partial genome fragment had high sequence identity to the other two and also belonged to the Africa 2 lineage. Almost half of the study participants practiced dog consumption [49% (265/541)]. Males were almost twice (cOR = 1.72, 95% CI (1.17-2.52), p-value = .006) as likely to consume dog meat compared to females. Likewise, the Frafra tribe from northern Ghana [cOR = 825.1, 95% CI (185.3-3672.9), p-value < .0001] and those with non-specific tribes [cOR = 47.05, 95% CI (10.18-217.41), p-value < .0001] presented with higher odds of dog consumption compared to Ewes. The butchers used bare hands in meat preparation. This study demonstrates the presence of rabies virus RNA in apparently healthy dogs slaughtered for human consumption in Ghana and suggests a potential risk for rabies transmission. Veterinary departments and local assemblies are recommended to monitor and regulate this practice

Genomic Characterization and Antimicrobial Susceptibility of Dromedary-Associated Staphylococcaceae from the Horn of Africa.

Members of the Staphylococcaceae family, particularly those of the genus Staphylococcus, encompass important human and animal pathogens. We collected and characterized Staphylococcaceae strains from apparently healthy and diseased camels (n = 84) and cattle (n = 7) in Somalia and Kenya. We phenotypically characterized the strains, including their antimicrobial inhibitory concentrations. Then, we sequenced their genomes using long-read sequencing, closed their genomes, and subsequently compared and mapped their virulence- and resistance-associated gene pools. Genome-based phylogenetics revealed 13 known Staphylococcaceae and at least two novel species. East African strains of different species encompassed novel sequence types and phylogenetically distant clades. About one-third of the strains had non-wild-type MICs. They were resistant to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, gentamicin, or streptomycin, encoded by tet(K), blaZ/blaARL, mecA/mecA1, msrA/mphC, salA, dfrG, aacA-aphD, and str, respectively. We identified the first methicillin- and multidrug-resistant camel S. epidermidis strain of sequence type (ST) 1136 in East Africa. The pool of virulence-encoding genes was largest in the S. aureus strains, as expected, although other rather commensal strains contained distinct virulence-encoding genes. We identified toxin-antitoxin (TA) systems such as the hicA/hicB and abiEii/abiEi families, reported here for the first time for certain species of Staphylococcaceae. All strains contained at least one intact prophage sequence, mainly belonging to the Siphoviridae family. We pinpointed potential horizontal gene transfers between camel and cattle strains and also across distinct Staphylococcaceae clades and species. IMPORTANCE Camels are a high value and crucial livestock species in arid and semiarid regions of Africa and gain importance giving the impact of climate change on traditional livestock species. Our current knowledge with respect to Staphylococcaceae infecting camels is very limited compared to that for other livestock species. Better knowledge will foster the development of specific diagnostic assays, guide promising antimicrobial treatment options, and inform about potential zoonotic risks. We characterized 84 Staphylococcaceae strains isolated from camels with respect to their antimicrobial resistance and virulence traits. We detected potentially novel Staphylococcus species, resistances to different classes of antimicrobials, and the first camel multidrug-resistant S. epidermidis strain of sequence type 1136

Causes of death and comorbidities in hospitalized patients with COVID-19

Infection by the new corona virus strain SARS-CoV-2 and its related syndrome COVID-19 has been associated with more than two million deaths worldwide. Patients of higher age and with preexisting chronic health conditions are at an increased risk of fatal disease outcome. However, detailed information on causes of death and the contribution of pre-existing health conditions to death yet is missing, which can be reliably established by autopsy only. We performed full body autopsies on 26 patients that had died after SARS-CoV-2 infection and COVID-19 at the Charite University Hospital Berlin, Germany, or at associated teaching hospitals. We systematically evaluated causes of death and pre-existing health conditions. Additionally, clinical records and death certificates were evaluated. We report findings on causes of death and comorbidities of 26 decedents that had clinically presented with severe COVID-19. We found that septic shock and multi organ failure was the most common immediate cause of death, often due to suppurative pulmonary infection. Respiratory failure due to diffuse alveolar damage presented as immediate cause of death in fewer cases. Several comorbidities, such as hypertension, ischemic heart disease, and obesity were present in the vast majority of patients. Our findings reveal that causes of death were directly related to COVID-19 in the majority of decedents, while they appear not to be an immediate result of preexisting health conditions and comorbidities. We therefore suggest that the majority of patients had died of COVID-19 with only contributory implications of preexisting health conditions to the mechanism of death

Type of vaccine and immunosuppressive therapy but not diagnosis critically influence antibody response after COVID-19 vaccination in patients with rheumatic disease

Objective: The development of sufficient COVID-19 vaccines has been a big breakthrough in fighting the global SARS-CoV-2 pandemic. However, vaccination effectiveness can be reduced in patients with autoimmune rheumatic diseases (AIRD). The aim of this study was to identify factors that lead to a diminished humoral vaccination response in patients with AIRD. Methods: Vaccination response was measured with a surrogate virus neutralisation test and by testing for antibodies directed against the receptor-binding-domain (RBD) of SARS-CoV-2 in 308 fully vaccinated patients with AIRD. In addition, 296 immunocompetent participants were investigated as a control group. Statistical adjusted analysis included covariates with a possible influence on antibody response. Results: Patients with AIRD showed lower antibody responses compared with immunocompetent individuals (median neutralising capacity 90.8% vs 96.5%, p<0.001; median anti-RBD-IgG 5.6 S/CO vs 6.7 S/CO, p<0.001). Lower antibody response was significantly influenced by type of immunosuppressive therapy, but not by rheumatic diagnosis, with patients under rituximab therapy developing the lowest antibody levels. Patients receiving mycophenolate, methotrexate or janus kinase inhibitors also showed reduced vaccination responses. Additional negative influencing factors were vaccination with AZD1222, old age and shorter intervals between the first two vaccinations. Conclusion: Certain immunosuppressive therapies are associated with lower antibody responses after vaccination. Additional factors such as vaccine type, age and vaccination interval should be taken into account. We recommend antibody testing in at-risk patients with AIRD and emphasise the importance of booster vaccinations in these patients

Autochthonous West Nile virus infection in Germany: Increasing numbers and a rare encephalitis case in a kidney transplant recipient.

West Nile Virus (WNV) infections are increasingly detected in birds and horses in central Europe, with the first mosquito-borne autochthonous human infection detected in Germany in 2019. Human infections are typically asymptomatic, with occasional severe neurological disease. Because of a low number of cases in central Europe, awareness regarding potential cases is low and WNV diagnostic testing is not routine. We tested cerebrospinal fluid (CSF) samples from unsolved encephalitis and meningitis cases from Berlin from 2019 to 2020, and describe a WNV-encephalitis case in a 33-year-old kidney transplant recipient. The infectious course was resolved by serology, RT-PCR and sequencing of stored samples. Phylogenetic sequence analysis revealed a close relationship of the patient's WNV strain to German sequences from 2019 and 2020. A lack of travel history and patient self-isolation during the SARS-CoV-2 pandemic suggest the infection was acquired in the patient's home or garden. Serological tests of four people sharing the living space were negative. Retrospective RT-PCR and WNV-IgM testing of 671 CSF samples from unsolved encephalitis and meningitis cases from Berlin detected no additional infections. The recent increase of WNV cases illustrates the importance of considering WNV in cases of meningoencephalitis, especially in immunocompromised patients, as described here. Proper education and communication and a revised diagnostic strategy will help to raise awareness and to detect future WNV infections

Amplification of Emerging Viruses in a Bat Colony

Concentration and prevalence of coronaviruses and astroviruses increase when bats form maternity roosts and bear young