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The SARS-CoV-2 Delta variant, corresponding to the Pangolin lineage B.1.617.2, was first detected in India in July 2020 and rapidly became dominant worldwide. The ARTIC v3 protocol for SARS-CoV-2 whole-genome sequencing, which relies on a large number of PCR primers, was among the first available early in the pandemic, but may be prone to coverage dropouts that result in incomplete genome sequences. A new set of primers (v4) was designed to circumvent this issue in June 2021. In this study, we investigated whether the sequencing community adopted the new sets of primers, especially in the context of the spread of the Delta lineage, in July 2021. Because information about protocols from individual laboratories is generally difficult to obtain, the aims of the study were to identify whether large under-sequenced regions were present in deposited Delta variant genome sequences (from April to August 2021), to investigate the extent of the coverage dropout among all the currently available Delta sequences in six countries, and to propose simple PCR primer modifications to sequence the missing region, especially for the first circulating Delta variants observed in 2021 in Switzerland. Candidate primers were tested on few clinical samples, highlighting the need to further pursue primer optimization and validation on a larger and diverse set of samples.

Supplemental material, sj-pdf-1-tan-10.1177_17562864221080528 for Neuro-axonal injury in COVID-19: the role of systemic inflammation and SARS-CoV-2 specific immune response by C��dric Hirzel, Denis Grandgirard, Bernard Surial, Manon F. Wider, David Leppert, Jens Kuhle, Laura N. Walti, Joerg C. Schefold, Thibaud Spinetti, Franziska Suter-Riniker, Ronald Dijkman and Stephen L. Leib in Therapeutic Advances in Neurological Disorders

Supplemental material, sj-pdf-2-tan-10.1177_17562864221080528 for Neuro-axonal injury in COVID-19: the role of systemic inflammation and SARS-CoV-2 specific immune response by C��dric Hirzel, Denis Grandgirard, Bernard Surial, Manon F. Wider, David Leppert, Jens Kuhle, Laura N. Walti, Joerg C. Schefold, Thibaud Spinetti, Franziska Suter-Riniker, Ronald Dijkman and Stephen L. Leib in Therapeutic Advances in Neurological Disorders

Viral cross-species transmission is recognized to be a major threat to both human and animal health, however detailed information on determinants underlying virus host tropism and susceptibility is missing. Influenza C and D viruses (ICV, IDV) are two respiratory viruses that share up to 50% genetic similarity, and both employ 9-O-acetylated sialic acids to enter a host cell. While ICV infections are mainly restricted to humans, IDV possesses a much broader host tropism and has shown to have a zoonotic potential. This suggests that additional virus-host interactions play an important role in the distinct host spectrum of ICV and IDV. In this study, we aimed to characterize the innate immune response of the respiratory epithelium of biologically relevant host species during influenza virus infection to identify possible determinants involved in viral cross-species transmission. To this end, we performed a detailed characterization of ICV and IDV infection in primary airway epithelial cell (AEC) cultures from human, porcine, and bovine origin. We monitored virus replication kinetics, cellular and host tropism, as well as the host transcriptional response over time at distinct ambient temperatures. We observed that both ICV and IDV predominantly infect ciliated cells, independently from host and temperature. Interestingly, temperature had a profound influence on ICV replication in both porcine and bovine AEC cultures, while IDV replicated efficiently irrespective of temperature and host. Detailed time-resolved transcriptome analysis revealed both species-specific and species uniform host responses and highlighted 34 innate immune-related genes with clear virus-specific and temperature-dependent profiles. These data provide the first comprehensive insights into important common and species-specific virus-host dynamics underlying the distinct host tropism of ICV and IDV, as well as possible determinants involved in viral cross-species transmission.

Background Protests and police fieldwork provides a high exposure environment for SARS-CoV-2 infections. In this cross-sectional analysis, we investigated the seroprevalence among a police cohort, and sociodemographic, work and health-related factors associated with seropositivity. Methods Study participants were invited for serological testing of SARS-CoV-2 and to complete online questionnaires. Serum neutralization titres towards the wild-type SARS-CoV-2 spike protein (expressing D614G) and the alpha and beta variants were measured in seropositive study participants. Results 978 police personnel representing 35% of the entire staff participated from February to March 2021. The seroprevalence was 12.9%. It varied by geographic region within the canton; ranged from 9% to 13.5% in three regions, including the city; and was 22% in Bernese Seeland/Jura with higher odds for seropositivity (OR 2.38, 95% CI 1.28���4.44, P=0.006). Job roles with mainly office activity were associated with a lower risk of seropositivity (0.33, 0.14���0.77, P=0.010). Most seropositive employees (67.5%) reported having had COVID-19 three months or longer prior to serological testing. Selfreported compliance with mask wearing during working hours was 100%; 45% of all seropositive versus 5% of all seronegative participants (P

Background Protests and police fieldwork provide a high-exposure environment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. In this cross-sectional analysis, we investigated the seroprevalence among a police cohort, and sociodemographic, work, and health-related factors associated with seropositivity. Methods Study participants were invited for serological testing of SARS-CoV-2 and to complete online questionnaires. Serum neutralization titers toward the wild-type SARS-CoV-2 spike protein (expressing D614G) and the Alpha and Beta variants were measured in seropositive study participants. Results A total of 978 police personnel representing 35% of the entire staff participated from February to March 2021. The seroprevalence was 12.9%. It varied by geographic region, ranged from 9% to 13.5% in 3 regions, including the city; and was 22% in Bernese Seeland/Jura with higher odds for seropositivity (odds ratio [OR], 2.38 [95% confidence interval {CI}, 1.28–4.44], P=.006). Job roles with mainly office activity were associated with a lower risk of seropositivity (OR, 0.33 [95% CI, .14–.77], P=.010). Self-reported compliance with mask wearing during working hours was 100%; 45% of seropositive vs 5% of seronegative participants (P, The seroprevalence of anti–SARS-CoV-2 antibodies of police officers was comparable to that reported in the general population. The level of serum antibody titers correlates well with neutralization capacity. Low antibody titers acquired from natural infection are not effective against variants.

The prevention of bovine respiratory disease is important, as it may lead to impaired welfare, economic losses, and considerable antimicrobial use, which can be associated with antimicrobial resistance. The aim of this study was to describe the prevalence of respiratory viruses and to identify risk factors for their occurrence. A convenience sample of 764 deep nasopharyngeal swab samples from veal calves was screened by PCR for bovine respiratory syncytial virus (BRSV), bovine parainfluenza-3 virus (BPI3V), bovine coronavirus (BCoV), influenza D virus (IDV), and influenza C virus (ICV). The following prevalence rates were observed: BRSV, 2.1%, BPI3V, 3.3%, BCoV, 53.5%, IDV, 4.1%, ICV, 0%. Logistic mixed regression models were built for BCoV to explore associations with calf management and housing. Positive swab samples were more frequent in younger calves than older calves (&gt, 100 days, p &lt, 0.001). The probability of detecting BCoV increased with increasing group size in young calves. Findings from this study suggested that young calves should be fattened in small groups to limit the risk of occurrence of BCoV, although an extended spectrum of risk factors for viral associated respiratory disorders such as nutritional aspects should be considered in future studies.

Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human upper and lower respiratory tract (33°C and 37°C, respectively) have been shown to affect the replication kinetics of several respiratory viruses, as well as host innate immune response dynamics, we investigated the impact of temperature on SARS-CoV-2 and SARS-CoV infection using the primary human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated to higher titers when infections were performed at 33°C rather than 37°C. Although both viruses were highly sensitive to type I and type III interferon pretreatment, a detailed time-resolved transcriptome analysis revealed temperature-dependent interferon and pro-inflammatory responses induced by SARS-CoV-2 that were inversely proportional to its replication efficiency at 33°C or 37°C. These data provide crucial insight on pivotal virus–host interaction dynamics and are in line with characteristic clinical features of SARS-CoV-2 and SARS-CoV, as well as their respective transmission efficiencies., The temperature in the lower respiratory tract is higher than in the upper respiratory tract. This study compares the viral replication kinetics and host cell response during SARS-CoV-2 and SARS-CoV infection, finding that the temperature of the human respiratory epithelium influences the viral replication and virus-host dynamics of SARS-CoV-2, but not of SARS-CoV.