Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave

The COVID-19 pandemic first emerged in Malaysia in Jan 2020. As of 12th Sept 2021, 1,979,698 COVID-19 cases that occurred over three major epidemic waves were confirmed. The virus contributing to the three epidemic waves has not been well-studied. We sequenced the genome of 22 SARS-CoV-2 strains detected in Malaysia during the second and the ongoing third wave of the COVID-19 epidemic. Detailed phylogenetic and genetic variation analyses of the SARS-CoV-2 isolate genomes were performed using these newly determined sequences and all other available sequences. Results from the analyses suggested multiple independent introductions of SARS-CoV-2 into Malaysia. A new B.1.524(G) lineage with S-D614G mutation was detected in Sabah, East Malaysia and Selangor, Peninsular Malaysia on 7th October 2020 and 14th October 2020, respectively. This new B.1.524(G) group was not the direct descendant of any of the previously detected lineages. The new B.1.524(G) carried a set of genetic variations, including A701V (position variant frequency = 0.0007) in Spike protein and a novel G114T mutation at the 5’UTR. The biological importance of the specific mutations remained unknown. The sequential appearance of the mutations, however, suggests that the spread of the new B.1.524(G) lineages likely begun in Sabah and then spread to Selangor. The findings presented here support the importance of SARS-CoV-2 full genome sequencing as a tool to establish an epidemiological link between cases or clusters of COVID-19 worldwide.

Feasibility of SARS-CoV-2 Antibody Testing in Remote Outpatient Trials

Background During the Covid-19 pandemic, clinical trials necessitated rapid testing to be performed remotely. Dried blood spot (DBS) techniques have enabled remote HIV virologic testing globally and more recently, antibody testing as well. We evaluated DBS testing for SARS-CoV-2 antibody testing in outpatients to assess seropositivity. Methods In 2020, we conducted three internet-based randomized clinical trials and offered serologic testing via self-collected DBS as a voluntary sub-study. COVID-19 diagnosis was based on CDC case definition with epidemiological link to cases. A minority reported PCR testing at an outside facility. We tested for anti-SARS-CoV-2 immunoglobulin via Antibody Detection by Agglutination-PCR (ADAP) and compared with ELISA. Results Of 2727 participants in the primary studies, 60% (1648/2727) consented for serology testing; 56% (931/1648) returned a usable DBS sample. Of those asymptomatic, 5% (33/707) had positive ADAP serology. Of participants with a positive PCR, 67% (36/54) had positive SARS-CoV-2 antibodies. None of those who were PCR-positive and asymptomatic were seropositive (0/7). Of 77 specimens tested for concordance via ELISA, 83% (64/77) were concordant. Challenges of completing a remote testing program during a pandemic included sourcing and assembling collection kits, delivery and return of the kits, and troubleshooting testing. Self-collection was successful for >95% of participants. Delays in US mail with possible sample degradation and timing of DBS collection complicated the analysis. Conclusion We found remote antibody testing during a global pandemic feasible although challenging. We identified an association between symptomatic COVID-19 and positive antibody results at similar prevalence to other outpatient cohorts.

Outbreaks of mumps genotype G viruses in the Netherlands between October 2019 and March 2020: clusters associated with multiple introductions

Background From October 2019–March 2020, several clusters of mumps cases were identified in the Netherlands. Our objective was to describe cluster-associated mumps virus transmission using epidemiological and molecular information in order to help future mumps outbreak investigation and control efforts. Methods An epidemiological cluster includes ≥ 2 mumps cases with at least an epidemiological-link to a laboratory-confirmed mumps case. A molecular group includes ≥ 2 mumps cases with identical mumps virus sequences. Cases with symptom onset date between 1 October 2019 and 31 March 2020 reported through the National Notifiable Diseases Surveillance System were included. We described epidemiological and clinical characteristics of mumps cases. Sequence data was obtained from selected regions of mumps virus genomes (2270 nucleotides). Associations between epidemiological and molecular information were investigated. Results In total, 102 mumps cases were notified (90% laboratory-confirmed, 10% epidemiologically-linked). 71 out of 102 cases were identified as part of an epidemiological cluster and/or molecular group. Twenty-one (30%) of 71 cases were identified solely from epidemiological information, 25 (35%) solely from molecular surveillance, and 25 (35%) using both. Fourteen epidemiological clusters were identified containing a total of 46 (range: 2–12, median: 3) cases. Complete sequence data was obtained from 50 mumps genotype G viruses. Twelve molecular groups were identified containing 43 (range: 2–13) cases, dispersed geographically and timewise. Combined information grouped seven epidemiological clusters into two distinct molecular groups. The first lasting for 14 weeks, the other for 6. Additionally, one molecular group was detected, linked by geography and time but without an epidemiological-link. Conclusions Combined epidemiological and molecular information indicated ongoing mumps virus transmission from multiple introductions for extended time periods. Sequence analysis provided valuable insights into epidemiological clustering. If combined information is available in a timely manner, this would improve outbreak detection, generate further insight into mumps transmission, and guide necessary control measures.

CO-St (COVID 19- study): impact of the management of men versus women in the treatment of Covid 19. A Multi-Centric Observational study

Background: from December 2019 and the spreading of syndemics, a lot of medical centers reg-istered data about their patients. In Italy, the most relevant quantity of patients was hospitalized in internal medicine wards. Methods: In this observational, retrospective cross-sectional study, all data of the COVID-19 patients, admitted Latio hospitals, from March 01 to December 31, 2020, were collected and their Epidemiological data, demographics, signs and symptoms on admission, comorbidities, laboratory findings, chest radiography and CT findings, treatment received and mortality rate were analyzed by gender to find any differences of gravity of disease. Clinician details were registered on database (one for every hospital). Cost analysis was performed by length of stay and antiviral drugs use, using point of view of Italian Healthcare System. Results: 2256 patients with mean age of 71.01 ± 28.02 years were included. For men, frequency of hyper-tension, COPD, use of oxygen therapy, Tocilizumab were significantly higher and epidemiolog-ical link was related to rehabilitation ward and community. The gender difference about hospi-talization was one day more for man. No strong significant difference by gender in the death rate was observed. Considering antiviral drugs and hospitalization, a man costs €1000 more than woman. Conclusions: In male patients, hypertension and COPD were observed more frequently and the epidemiological link was related to rehabilitation ward and community. In female sub-jects, the epidemiological link was related to Hospital and we observed significantly higher atypical chest-X ray. Tocilizumab, oxygen therapy and antiviral drugs were prescribed more in male subjects. No differences by gender we report in other treatments and outcomes. Future studies should be analyzed to get a more comprehensive understanding of COVID-19 by gender.

Genetic evidence substantiates transmission of Trichinella spiralis from one swine farm to another

Background Trichinella spiralis ranks seventh in the risk posed by foodborne parasites. It causes most human cases of trichinellosis and is the most frequent cause of Trichinella outbreaks on pig farms and in wild boar, worldwide. Veterinary inspectors seek the source of outbreaks in hopes of limiting the spread. Established molecular tools are inadequate for distinguishing among potential T. spiralis infection sources because genetic variability in these zoonotic pathogens is limited in Europe. Microsatellite markers proved successful in tracing an outbreak of T. britovi, a related parasite harboring much more genetic variation. Here, we successfully employed microsatellite markers to determine the genetic structure of T. spiralis isolates from two pig outbreaks, discovering notable uniformity among parasites within each farm and discovering an epidemiological link between these two outbreaks. Methods The individual larvae from five isolates of T. spiralis from two pig farms and from ten wild boars were genotyped using nine microsatellite markers to examine their genetic structure. Results Notably uniform parasite populations constituted each farm outbreak, and the parasites from the first and second outbreaks resembled each other to a notable degree, indicating an epidemiological link between them. Wild boar harbored more genetically variable larval cohorts, distinguishing them from parasites isolated from domestic pigs. Conclusions Microsatellite markers succeeded in distinguishing isolates of the highly homogeneous T. spiralis, aiding efforts to track transmission. Each outbreak was composed of a homogenous group of parasites, suggesting a point source of contamination. Graphical abstract

A PARTICULAR CASE OF SARS-COV-2 INFECTION IN TWINS

Introduction. Although SARS-CoV-2 infection is more common in adults, many cases have been reported in the pediatric population. Case presentation. An 8-month-old infant from twin pregnancy, confirmed with COVID-19, is hospitalized with nasal obstruction, serous rhinorrhea, rare cough and watery stools. The epidemiological link is known, both the parents and the maternal grandparents of the infant being confirmed with COVID-19. Biologically, he presented with thrombocytosis and discrete inflammatory syndrome, and the lung radiograph did not show any lesions. At the same time, the twin sister was hospitalized, who presented a similar symptomatology, with a negative SARS-CoV-2 PCR test, but the lung radiograph showed specific lesions of COVID-19. During hospitalization, 2 more SARS-CoV-2 PCR tests were performed, but with negative results. The evolution of the twins was favorable under symptomatic treatment, respectively antibiotic and symptomatic treatment. Conclusion. SARS-CoV-2 infection may be asymptomatic, especially in infants and newborns, and has a lower prevalence.

The impact of National Containment Measures on a Pediatric Italian regional Hub for COVID-19, an observational study

Background Numerous studies described the epidemiological link and main clinical features of pediatric COVID-19, during the first pandemic period. Our study encompasses several different phases since the National Lockdown in Italy. The primary outcome is (I) to analyze the prevalence of positive NST (Nasopharyngeal Swab Test) among the largest Italian Pediatric cohort admitted to a single regional PED Hub for COVID-19 during an eight-month period. Secondary outcomes are: (II) the description of trend of admissions in our PED and (III) the categorization of the positive patients according to clinical manifestations and epidemiological link. Methods We described 316 patients with a positive NST for SARS-CoV2, on a total of 5001 nasopharyngeal swabs performed among 13,171 admissions at our PED, over a period starting from March 17th, 2020 to December 1st, 2020. Age, epidemiological link, clinical features and hospitalizations were analyzed according to different lockdown phases. Data were collected anonymously from electronic records and analyzed using SPSS 22.00 statistics software (Chicago, IL). Results Thirty-six percent of total admissions have been tested. During the post lockdown period, we performed the highest percentage of NST (Nasopharyngeal Swab Test) 49.7%, and among them 7.9% were positive. The prevalence of infection during a 10-month period was 2.3%. Mean age was 6.5 years old. Familial Link accounted for the 67.7% of infection, while Extrafamilial and Unknown link accounted for 17 and 14.9%, respectively. Familial link is predominant during all phases. Seventeen patients showed an intra-scholastic link, and the highest prevalence was observed in the 7–10 years age group, with a prevalence of 12.8% (5 patients). Fever was the most frequent symptom (66%), in particular among preschooler children aged 0–6 years (71.9%). Older children were more frequently symptomatic. Seven patients were admitted with MIS-C diagnosis. Conclusions Different levels of containment measures caused important changes in number of positive NST for SARS-CoV2. Familial link was predominant in our cohort, during all phases of Lockdown. The risk of being infected at home is four time greater than the risk of being infected from an extra familial individual. Further studies are needed to evaluate the clear impact of intra-scholastic link. The constant improvement in knowledge on onset symptoms and risk factor for SARS-CoV2 infection and its complications (e.g. MIS-C), can impact on number of hospitalizations, ICU admissions and early management.

Outbreak of OXA-48-producing Enterobacterales in a haematological ward associated with an uncommon environmental reservoir, France, 2016 to 2019

The hospital water environment, including the wastewater drainage system, is increasingly reported as a potential reservoir for carbapenemase-producing Enterobacterales (CPE). We investigated a persistent outbreak of OXA-48 CPE (primarily Citrobacter freundii) in a haematological ward of a French teaching hospital by epidemiological, microbiological and environmental methods. Between January 2016 and June 2019, we detected 37 new OXA-48 CPE-colonised and/or ‑infected patients in the haematological ward. In October 2017, a unit dedicated to CPE-colonised and/or ‑infected patients was created. Eleven additional sporadic acquisitions were identified after this date without any obvious epidemiological link between patients, except in one case. Environmental investigations of the haematological ward (June–August 2018) identified seven of 74 toilets and one of 39 drains positive for OXA-48 CPE (seven C. freundii, one Enterobacter sakazakii, one Escherichia coli). Whole genome comparisons identified a clonal dissemination of OXA-48-producing C. freundii from the hospital environment to patients. In addition to strict routine infection control measures, an intensive cleaning programme was performed (descaling and bleaching) and all toilet bowls and tanks were changed. These additional measures helped to contain the outbreak. This study highlights that toilets can be a possible source of transmission of OXA-48 CPE.

The COVID-19 Impact in Hospital Healthcare Workers: Development of an Occupational Health Risk Management Program

As with the SARS-CoV-1 outbreak in 2003–2004 and the MERS outbreak in 2012, there were early reports of frequent transmission to healthcare workers (HCW) in the SARS-CoV-2 pandemic. Our hospital center identified its first COVID-19 confirmed case on March 9, 2020, in a 6-day hospitalized patient. The first confirmed COVID-19 case in a HCW happened 3 days later, in a nurse with a probable epidemiological link related to the first confirmed patient. Our study’s first objective is to describe and characterize the impact of the first 3 months of the SARS-CoV-2 pandemic on the Centro Hospitalar Universitário Lisboa Norte (CHULN). Our second objective is to report the performance of the CHULN Occupational Health Department (OHD) and the impact of the pandemic on CHULN HCW and its adaptation across national, regional, and institutional epidemiological evolution. Over the first 3 months, 2,152 HCW were screened (which represent 29.8% of the total HCW population), grouped in 100 separate identifiable clusters, each one ranging from 2 to 98 HCW. The most prevalent profession screened were nurses (<i>n</i> = 800; 37.2%) followed by doctors (<i>n</i> = 634; 29.5%). The main source of potential infection and cluster generating screening procedures was co-worker related (<i>n</i> = 1,216; 56.5%). A patient source or a combined patient co-worker source was only accountable for 559 (26%) and 43 (2%) of cases, respectively. Our preliminary results demonstrate a lower infection rate among HCW than the ones commonly found in the literature. The main source of infection seemed to be co-worker related rather than patient related. New preventive strategies would have to be implemented in order to control SARS-CoV-2 spread.