Detection of SARS-CoV-2 in Wastewater Associated with Scientific Stations in Antarctica and Possible Risk for Wildlife (preprint)

Before December 2020, Antarctica had remained free of Covid-19 cases. The main concern during the pandemic was the limited health facilities available at Antarctic stations to deal with the disease, as well as the potential impact of SARS-CoV-2 on Antarctic wildlife through reverse zoonosis. In December 2020, 60 cases emerged in Chilean Antarctic stations, disrupting the summer campaign with ongoing isolation needs. The SARS-CoV-2 RNA was detected in the wastewater of several scientific stations. In Antarctica, treated wastewater is discharged directly into the seawater. No studies currently address recovery of infectious virus particles from treated wastewater, but their presence raises the risk of infecting wildlife and initiating new replication cycles. This study highlights the initial virus detection in wastewater from Antarctic stations, identifying viral RNA via RT-qPCR targeting various genomic regions. The virus's RNA was found in effluent from two wastewater plants at Maxwell Bay and O’Higgins Station on King George Island and the Antarctic Peninsula, respectively. This study explores the potential for reverse zoonotic transmission of SARS-CoV-2 from humans to Antarctic wildlife due to the direct release of viral particles into seawater. The implications of such transmission underscore the need for continued vigilance and research.

Scavengers as Prospective Sentinels of Viral Diversity: the Snowy Sheathbill Virome as a Potential Tool for Monitoring Virus Circulation, Lessons from Two Antarctic Expeditions.

Antarctica is a unique environment due to its extreme meteorological and geological conditions. In addition to this, its relative isolation from human influences has kept it undisturbed. This renders our limited understanding of its fauna and its associated microbial and viral communities a relevant knowledge gap to fill. This includes members of the order Charadriiformes such as snowy sheathbills. They are opportunistic predator/scavenger birds distributed on Antarctic and sub-Antarctic islands that are in frequent contact with other bird and mammal species. This makes them an interesting species for surveillance studies due to their high potential for the acquisition and transport of viruses. In this study, we performed whole-virome and targeted viral surveillance for coronaviruses, paramyxoviruses, and influenza viruses in snowy sheathbills from two locations, the Antarctic Peninsula and South Shetland. Our results suggest the potential role of this species as a sentinel for this region. We highlight the discovery of two human viruses, a member of the genus Sapovirus GII and a gammaherpesvirus, and a virus previously described in marine mammals. Here, we provide insight into a complex ecological picture. These data highlight the surveillance opportunities provided by Antarctic scavenger birds. IMPORTANCE This article describes whole-virome and targeted viral surveillance for coronaviruses, paramyxoviruses, and influenza viruses in snowy sheathbills from the Antarctic Peninsula and South Shetland. Our results suggest an important role of this species as a sentinel for this region. This species' RNA virome showcased a diversity of viruses likely tied to its interactions with assorted Antarctic fauna. We highlight the discovery of two viruses of likely human origin, one with an intestinal impact and another with oncogenic potential. Analysis of this data set detected a variety of viruses tied to various sources (from crustaceans to nonhuman mammals), depicting a complex viral landscape for this scavenger species.

Impact of COVID-19 in a Cohort of Patients With Inflammatory Intestinal Disease

BACKGROUND: There are few data on the outcome of COVID-19 in patients with IBD, none in the Chilean population. The aim of the study was to describe the demographic and clinical characteristics of patients with IBD who developed COVID-19, the evolution and clinical course of IBD at 1 month follow-up after SARS-CoV-2 infection. METHOD(S): This was an observational, cross-sectional, and analytical study. Patients with positive RT-PCR SARS-Cov-2 who were followed in the IBD Program of Clinica las Condes tertiary referral center (n = 1,493), were studied by spontaneous patient consultation and/or email survey. The clinical IBD data and COVID-19 related symptoms were obtained from the medical record and follow-up telephone interviews. Statistical significance was determined (Fisher's test P < 0.05). RESULT(S): From March 1 to August 31, 2020, 32 patients were reported positive RT-PCR SARSCov- 2, 18 (56%) ulcerative colitis and 14 (44%) Crohn's disease. The median age was 32 years (range 18 - 69), 56% women. Seven patients had an additional comorbidities. At the time of infection, 9 patients and their co-habitants maintained quarantine, isolation and social distancing recommendations. Only 1 patient was clinically active at the time of infection. Ten patients (31%) were on immunomodulator/biologic maintenance treatment, of which 4 were on combination therapy. Sixty percent of patients contacted the IBD clinical team when RT-PCR SARS-Cov-2 resulted positive. The most frequent COVID-19 onset symptoms were headache (66%), myalgia (63%), and fever (50%). Four patients required hospitalization (no 1 in Critical Care Unit), none of them were on immunomodulator nor biologic treatment. Two patients received Azithromycin and 1 received steroids as treatment for COVID-19. In univariate analysis, there were no significant differences in age, diagnosis or IBD treatment in patients who required hospitalization for COVID-19 infection. Seven patients discontinued their IBD treatment during the infection (6 at the direction of the IBD Program and 1 self-discontinued therapy). Two patients had a flare of their IBD during 1 month post-COVID-19 follow-up. CONCLUSION(S): In this cohort of patients, IBD medications, including immunomodulators and biologic therapy, were not associated with a greater severity of COVID-19 infection.

Best practices during COVID-19 pandemic in solid organ transplant programs in Spain.

Clinical management of transplant patients abruptly changed during the first months of COVID-19 pandemic (March to May 2020). The new situation led to very significant challenges, such as new forms of relationship between healthcare providers and patients and other professionals, design of protocols to prevent disease transmission and treatment of infected patients, management of waiting lists and of transplant programs during state/city lockdown, relevant reduction of medical training and educational activities, halt or delays of ongoing research, etc. The two main objectives of the current report are: 1) to promote a project of best practices in transplantation taking advantage of the knowledge and experience acquired by professionals during the evolving situation of the COVID-19 pandemic, both in performing their usual care activity, as well as in the adjustments taken to adapt to the clinical context, and 2) to create a document that collects these best practices, thus allowing the creation of a useful compendium for the exchange of knowledge between different Transplant Units. The scientific committee and expert panel finally standardized 30 best practices, including for the pretransplant period (n = 9), peritransplant period (n = 7), postransplant period (n = 8) and training and communication (n = 6). Many aspects of hospitals and units networking, telematic approaches, patient care, value-based medicine, hospitalization, and outpatient visit strategies, training for novelties and communication skills were covered. Massive vaccination has greatly improved the outcomes of the pandemic, with a decrease in severe cases requiring intensive care and a reduction in mortality. However, suboptimal responses to vaccines have been observed in transplant recipients, and health care strategic plans are necessary in these vulnerable populations. The best practices contained in this expert panel report may aid to their broader implementation.

Best practices during COVID-19 pandemic in solid organ transplant programs in Spain

Clinical management of transplant patients abruptly changed during the first months of COVID-19 pandemic (March to May 2020). The new situation led to very significant challenges, such as new forms of relationship between healthcare providers and patients and other professionals, design of protocols to prevent disease transmission and treatment of infected patients, management of waiting lists and of transplant programs during state/city lockdown, relevant reduction of medical training and educational activities, halt or delays of ongoing research, etc. The two main objectives of the current report are: 1) to promote a project of best practices in transplantation taking advantage of the knowledge and experience acquired by professionals during the evolving situation of the COVID-19 pandemic, both in performing their usual care activity, as well as in the adjustments taken to adapt to the clinical context, and 2) to create a document that collects these best practices, thus allowing the creation of a useful compendium for the exchange of knowledge between different Transplant Units. The scientific committee and expert panel finally standardized 30 best practices, including for the pretransplant period (n = 9), peritransplant period (n = 7), postransplant period (n = 8) and training and communication (n = 6). Many aspects of hospitals and units networking, telematic approaches, patient care, value-based medicine, hospitalization, and outpatient visit strategies, training for novelties and communication skills were covered. Massive vaccination has greatly improved the outcomes of the pandemic, with a decrease in severe cases requiring intensive care and a reduction in mortality. However, suboptimal responses to vaccines have been observed in transplant recipients, and health care strategic plans are necessary in these vulnerable populations. The best practices contained in this expert panel report may aid to their broader implementation.

Surveillance of seasonal respiratory viruses among Chilean patients during the COVID-19 pandemic (preprint)

SARS-CoV-2 has generated over 122 million cases worldwide. Non-pharmaceuticals interventions such as confinements and lockdowns started in Chile on March 18th 2020. In Europe, confinements and lockdowns have been accompanied by a decrease in the circulation of other respiratory viruses such as Influenza A virus(IAV), Influenza B virus(IBV) or respiratory syncytial virus(RSV). Although changes in circulation patterns of respiratory viruses have been reported, limited information regarding the southern hemisphere is available where the SARS-CoV-2 pandemic merged with the winter season. We conducted viral surveillance of respiratory viruses and we evaluated their presence and establishing whether they were co-circulating with SARS-CoV-2.

Argentine Registry of neurological manifestations due to coronavirus-19 (COVID-19) (preprint)

COVID-19 disease has spread around the world since December 2019. Neurological symptoms are part of its clinical spectrum. Objective: To know the neurological manifestations in patients infected by COVID-19 in Argentina. Methods: Multicenter study conducted in adults, from May 2020 to January 2021, with confirmed COVID-19 and neurological symptoms. Demographic variables, existence of systemic or neurological comorbidities, the form of onset of the infection, alteration in complementary studies and the degree of severity of neurological symptoms were recorded. Results: 817 patients from all over the country were included, 52% male, mean age 38 years, most of them without comorbidities or previous neurological pathology. The first symptom of the infection was neurological in 56.2% of the cases, predominantly headache (69%), then anosmia / ageusia (66%). Myalgias (52%), allodynia / hyperalgesia (18%), and asthenia (6%) were also reported. 3.2% showed diffuse CNS involvement such as encephalopathy or seizures. 1.7% had cerebrovascular complications. Sleep disorders were observed in 3.2%. 6 patients were reported with Guillain Barre (GBS), peripheral neuropathy (3.4%), tongue paresthesia (0.6%), hearing loss (0.4%), plexopathy (0.3%). The severity of neurological symptoms was correlated with age and the existence of comorbidities. Conclusions: Our results, similar to those of other countries, show two types of neurological symptoms associated with COVID-19: some potentially disabling or fatal such as GBS or encephalitis, and others less devastating, but more frequent such as headache or anosmia that demand increasingly long-term care.

Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile.

Chile has one of the worst numbers worldwide in terms of SARS-CoV-2 positive cases and COVID-19-related deaths per million inhabitants; thus, characterization of neutralizing antibody (NAb) responses in the general population is critical to understanding of immunity at the local level. Given our inability to perform massive classical neutralization assays due to the scarce availability of BSL-3 facilities in the country, we developed and fully characterized an HIV-based SARS-CoV-2 pseudotype, which was used in a 96-well plate format to investigate NAb responses in samples from individuals exposed to SARS-CoV-2 or treated with convalescent plasma. We also identified samples with decreased or enhanced neutralization activity against the D614G spike variant compared with the wild type, indicating the relevance of this variant in host immunity. The data presented here represent the first insights into NAb responses in individuals from Chile, serving as a guide for future studies in the country.

P.247 Psychological impact of COVID-19 confinement among people with history of mental disorders (bipolar, anxiety, depression) and general population in Spain

Background: Previous studies have shown that epidemic outbreaks have significant effects on mental health and psychological wellbeing, increasing psychiatric morbidity among population [1]. During the initial phase of the COVID-19 outbreak in China, more than half of the general population reported a strong psychological impact and approximately a third moderate to severe anxiety [2]. Furthermore, there is evidence that the psychological effects of infection outbreaks can affect months or years later [3]. A better understanding of the psychological impact of the COVID-19 outbreak is crucial to design coping programs that may mitigate these responses during such outbreaks. Aim: The objective of this study is to determine the early impact of the COVID-19 on mental health among people with history of mental disorders (anxiety, depression and bipolar disorder) and the General Population and people in Spain. Methods: In this study 252 people were included. Sixty three people with a history of bipolar disorder (hBD) were matched by sex and gender with 63 people with a history of anxiety disorders (hAD), 63 people with a history of depression (hDD) and 63 healthy controls (HC). The assessment was made by an online survey during the first days of the national lockdown due to COVID-19 (from 19 March to 26 March 2020) in Spain. Assessment: ad hoc sociodemographic, physical and clinical data questionnaire and the Spanish versions of the Depression, Anxiety and Stress Scale (DASS-21) and the Impact of Event Scale (IES). Results: Mean age was 45 (range 19-69, SD 14.8) years;69.8% were females for the total example and the four groups. Regarding clinical symptoms, 61.9%hBD, 54.0% hAD, 54.0% hDD and 28.6% HC reported depressive symptoms (χ² =15.922, p <0.001);19.0% hBD, 12.7% hAD, 20.6% hDD and 1.6% HC reported anxiety symptoms (χ² =12.104, p = 0.007);38.1%hBD, 34.9% hAD, 41.3% hDD and 19.0% HC reported stress symptoms (χ² =8.286, p = 0.040). Regarding psychological impact, 27.0%hBD, 17.5% hAD, 25.4% hDD and 14.3% HC reported intrusion style (χ² =4.277, p =0.273);38.1% hBD, 47.6% hAD, 57.1% hDD and 30.2% HC reported avoidance style (χ² =10.525, p =0.015). There were differences between groups in the three DASS-21 subscales scores: Depression (F=4.599, p= 0.004), Anxiety (F = 5.443, p <0.001) and Stress (F=3.537, p = 0.015) and in the IES total score (F=6.018, p<0.001) and each IES subscale: Intrusion (F=3.030, p = 0.030) and Avoidance (F=6.041, p <0.001). Conclusions: The emergency confinement by COVID-19 has an impact on mental health, but especially among people with history of mental disorders (anxiety, depression and bipolar disorder). Depressive symptoms were the most frequent symptoms in all groups, followed by stress symptoms. People with history of Bipolar Disorder was the group with the highest percentage of depressive symptoms. The most frequent style was avoidance in all groups. People with history of Bipolar Disorder was the group with the highest percentage of people with an intrusion style. People with history of Depression Disorder was the group with the highest percentage of people with an avoidance style. No conflict of interest

Accuracy of a RT-qPCR SARS-CoV-2 detection assay without prior RNA extraction.

The current COVID-19 pandemic constitutes a threat to the population worldwide with over 21 million infected people. There is an urgent need for the development of rapid and massive detection tools as well as the identification and isolation of infected individuals. we sought to evaluate different RT-qPCR kits and protocols to evaluate the best approach to be used omitting an RNA extraction step. We have investigated the sensitivity and performance of different commercially available RT-qPCR kits in detecting SARS-CoV-2 using 80 extracted RNA and NSS from COVID-19 diagnosed patients. We evaluated the ability of each kit to detect viral RNA from both kit-extracted or directly from a pre-boiled NSS observing that direct RNA detection is possible when Ct values are lower than 30 with the three kits tested. Since SARS-CoV-2 testing in most locations occurs once COVID-19 symptoms are evident and, therefore, viral loads are expected to be high, our protocol will be useful in supporting SARS-CoV-2 diagnosis, especially in America where COVID-19 cases have exploded in the recent weeks as well as in low- and middle-income countries, which would not have massive access to kit-based diagnosis. The information provided in this work paves the way for the development of more efficient SARS-CoV-2 detection approaches avoiding an RNA extraction step.

SARS-CoV-2 Detection in Sewage in Santiago, Chile - Preliminary results. (preprint)

The detection of viruses in sewage is a method of environmental surveillance, which allows evaluating the circulation of different viruses in a community. This study presents the first results of sewage surveillance to detect the circulation of SARS-CoV-2 virus in Santiago, Chile. Using ultracentrifugation associated with RT-qPCR, we detected SARS-CoV-2 in untreated and treated wastewater samples obtained two treatment plants, which together process around 85% of the wastewater from the city. This is the first report of detection of SARS-CoV-2 in sewage in Chile and indicates that wastewater surveillance could be a sensitive tool useful as a predictive marker of the circulation of the virus in a population and therefore, be used as an early warning tool.

SARS-CoV-2 detection from nasopharyngeal swab samples without RNA extraction (preprint)

The ongoing COVID-19 pandemic has reached more than 200 countries and territories worldwide. Given the large requirement of SARS-CoV-2 diagnosis and considering that RNA extraction kits are in short supply, we investigated whether two commercial RT-qPCR kits were compatible with direct SARS-CoV-2 detection from nasopharyngeal swab samples. We show that one of the tested kits is fully compatible with direct SARS-CoV-2 detection suggesting that omission of an RNA extraction step should be considered in SARS-CoV-2 diagnosis.