Severe Acute Respiratory Syndrome Coronavirus 2 Outbreak Related to a Nightclub, Germany, 2020

SARS-CoV-2 transmission dynamics in bars, restaurants, and nightclubs

Background

In an attempt to control the spread of SARS-CoV-2, many governments decided to close public venues including bars, restaurants, and nightclubs during the pandemic, making it difficult to study how transmission occurs in these environments. In this study, we were able to gain insight into the transmission dynamics of SARS-CoV-2 in 16 venues in the city of Maastricht using a combination of epidemiological and whole-genome sequencing (WGS) data during a period of 2 weeks in 2021, when bars, restaurants, and nightclubs were temporarily reopened in the Netherlands. This led to a subsequent rise of SARS-CoV-2 cases in the community following the reopening.

Methods

WGS was performed on samples from 154/348 of selected cases and combined with epidemiological investigation (e.g., contact tracing and linking cases to specific venues) to identify SARS-CoV-2 transmission clusters. In addition, genomic surveillance data were used to investigate spillover of outbreak-associated genotypes into the community.

Results

Clustering was observed in 129/136 (95%) successfully genotyped samples. We established that most cases were linked to venues with dancing facilities and that specific genotypes of the Delta variant were more frequently spread within and from these venues compared to venues without dancing facilities. In addition, we show indications of spillover of certain genotypes from the bar and restaurant industry into the community, with the number of hospital admissions increasing in the weeks following peak cases in the community.

Conclusion

Lifting restrictions on bar and restaurant industry venues with a corona entree ticket in a largely unvaccinated population led to a surge in COVID-19 cases and promoted the spread of new (sub)variants. Nightclubs were identified as potential super-spreading locations.

The future of evolutionary medicine: sparking innovation in biomedicine and public health

Evolutionary medicine - i.e. the application of insights from evolution and ecology to biomedicine - has tremendous untapped potential to spark transformational innovation in biomedical research, clinical care and public health. Fundamentally, a systematic mapping across the full diversity of life is required to identify animal model systems for disease vulnerability, resistance, and counter-resistance that could lead to novel clinical treatments. Evolutionary dynamics should guide novel therapeutic approaches that target the development of treatment resistance in cancers (e.g., via adaptive or extinction therapy) and antimicrobial resistance (e.g., via innovations in chemistry, antimicrobial usage, and phage therapy). With respect to public health, the insight that many modern human pathologies (e.g., obesity) result from mismatches between the ecologies in which we evolved and our modern environments has important implications for disease prevention. Life-history evolution can also shed important light on patterns of disease burden, for example in reproductive health. Experience during the COVID-19 (SARS-CoV-2) pandemic has underlined the critical role of evolutionary dynamics (e.g., with respect to virulence and transmissibility) in predicting and managing this and future pandemics, and in using evolutionary principles to understand and address aspects of human behavior that impede biomedical innovation and public health (e.g., unhealthy behaviors and vaccine hesitancy). In conclusion, greater interdisciplinary collaboration is vital to systematically leverage the insight-generating power of evolutionary medicine to better understand, prevent, and treat existing and emerging threats to human, animal, and planetary health.

A SARS-CoV-2 outbreak associated with five air force bases and a nightclub following the lifting of COVID-19-related social restrictions, United Kingdom, July-to-September 2021

We describe the management of two linked severe acute respiratory coronavirus 2 (SARS-CoV-2) outbreaks, predominantly amongst 18-35-year-olds, in a UK county in July-to-September 2021, following the lifting of national coronavirus disease 2019 (COVID-19)-associated social restrictions. One was associated with a nightclub and one with five air force bases. On week beginning 2nd August 2021, air force contact tracing teams detected 68 cases across five bases within one county; 21 (30.9%) were associated with a night-time economy venue, 13 (19.1%) with night-time economy venues in the county's main town and at least one case per base (n = 6, 8.8%) with a particular nightclub in this town, which itself had been associated with 302 cases in the previous week (coinciding with its reopening following a national lockdown). In response, Public Health England/United Kingdom Health Security Agency, air force and local authority teams collaboratively implemented communication strategies and enhanced access to SARS-CoV-2 testing and vaccination. Key challenges included attempting to encourage behaviours that reduce likelihood of transmission to a population who may have considered themselves at low risk from severe COVID-19. This report may inform future preparation for, and management of, easing of potential future pandemic-related social restrictions, and how an outbreak in this context may be addressed.

Lessons from a Year of COVID-19 in Zambia: Reported Attendance and Mask Wearing at Large Gatherings in Rural Communities

Zambia instituted prevention behavior guidelines for social gatherings before the first case of COVID-19 was confirmed on March 18, 2020. Guidelines included nonpharmaceutical interventions (NPIs) including mask wearing, social distancing, and reducing sizes of gatherings. Within a larger cluster randomized trial of community-based parenting groups in four rural districts (three in Southern Province, one in Eastern Province), we collected 5,711 questionnaires from intervention participants between August 2020 and September 2021, during which the country saw two COVID-19 waves. Questionnaires asked about participation and behaviors at community gatherings. Generally, perception of risk of contracting COVID-19 was low for respondents in districts in Southern Province but higher for those in Eastern Province. The highest compliance to mask wearing was reported at clinics (84%) and church services (81%), which were the most frequently attended gatherings. Many funerals were attended by 200 to 300 people, but individuals were 30% less likely to report wearing masks (odds ratio [OR] = 0.71, 95% confidence ratio [CI]: 0.6-0.8) than those attending a clinic visit. After controlling for other variables, the odds of self-reported mask wearing at events were higher in January to March 2021 (adjusted OR = 1.5, 95% CI: 1.3, 1.7) and July and September of 2021 (adjusted OR = 3.0, 95% CI: 2.5-3.5), timepoints that broadly overlay with two COVID-19 peaks observed in Zambia. Results suggest guideline dissemination penetrated the rural areas. However, there is need to optimize the messaging to increase compliance to NPIs at high-risk gatherings, including funerals. The findings from this analysis should be considered as the COVID-19 pandemic continues to evolve.

Risky Party and Nightclub Attendance during the COVID-19 Nightlife Shutdown in New York City

From March 2020 through May 2021, nightlife venues were shut down and large gatherings were deemed illegal in New York City (NYC) due to COVID-19. This study sought to determine the extent of risky party attendance during the COVID-19 shutdown among people who attend electronic dance music parties in NYC. During the first four months that venues were permitted to reopen (June through September 2021), time-space sampling was used to survey adults (n = 278) about their party attendance during the first year of the shutdown (March 2020-March 2021). We examined prevalence and correlates of attendance and mask-wearing at such parties. A total of 43.9% attended private parties with more than 10 people, 27.3% attended nightclubs, and 20.5% attended other parties such as raves. Among those who attended any, 32.3% never wore a mask and 19.3% reported attending parties in which no one wore a mask. Past-year ecstasy use was associated with increased risk for attending private (aPR = 1.51, 95% CI: 1.00-2.28) or other parties (aPR = 2.75, 95% CI: 1.48-5.13), and use of 2C series drugs was associated with increased risk for attending nightclubs (aPR = 2.67, 95% CI: 1.24-5.77) or other parties (aPR = 2.50, 95% CI: 1.06-5.87). Attending >10 parties was associated with increased risk for never wearing a mask (aPR = 2.74, 95% CI: 1.11-6.75) and for no other attendees wearing masks (aPR = 4.22, 95% CI: 1.26-14.07). Illegal dance parties continued in NYC during the COVID-19 shutdown. Prevention and harm reduction efforts to mitigate risk of COVID-19 transmission during such shutdowns are sorely needed.

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.

Initial Experience With SARS-CoV-2-Neutralizing Monoclonal Antibodies in Kidney or Combined Kidney-Pancreas Transplant Recipients

Background: Antiviral drugs have shown little impact in patient infected with acute respiratory coronavirus 2 (SARS-CoV-2). Especially for immunocompromised persons positive for SARS-CoV-2, novel treatments are warranted. Recently, the U.S. FDA has granted an emergency use authorization (EUA) to two monoclonal antibodies (mAb) targeting the viral spike protein: bamlanivimab and casivirimab and imdevimab. As per the EUA, all SARS-CoV-2 positive organ transplant recipients can receive mAb treatment. Patients and methods: We queried our center's transplant registry to identify SARS-CoV-2 infected recipients treated with single doses of either Bamlanivimab or casivirimab/imdevimab up to May 31, 2021. We analyzed clinical outcomes, renal function and virus-specific antibodies. The co-primary endpoints were hospitalization due to COVID-19 and SARS-CoV-2 RT-PCR negativity. Results: Thirteen patients at a median interval of 55 (IQR, 26-110) months from transplant were treated: 8 with bamlanivimab and 5 with casivirimab/imdevimab. In all, 4/13 (31%) patients were hospitalized at some time, while 11/13 (85%) achieved PCR negativity. 2/4 hospitalized patients received mAb as rescue treatment. Overall mortality was 23%, with one death attributable to transplant-associated lymphoma. All six patients infected with the B 1.1.7 variant were alive at last contact. Conclusion: mAb treatment appears effective when administered early to SARS-CoV-2-infected transplant recipients.

Risk Stratification of SARS-CoV-2 Breakthrough Infections Based on an Outbreak at a Student Festive Event

In early 2022, the Coronavirus disease 2019 (COVID-19) remains a global challenge. COVID-19 is caused by an increasing number of variants of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we report an outbreak of SARS-CoV-2 breakthrough infections related to a student festive event with 100 mostly vaccinated guests, which took place in Northern Bavaria, Germany, in October 2021. The data were obtained by retrospective guest interviews. In total, 95 students participated in the study, with 94 being fully vaccinated and 24 reporting infection by the delta variant. Correlation analyses among 15 examined variables revealed that time spent at the event, conversation with the supposed index person, and a homologous viral vector vaccination regime were significant risk factors for infection. Non-significant observations related to higher rates of infection included time since last vaccination, shared use of drinking vessels, and number of individual person-to-person contacts at the event. Our data suggest that a high rate of breakthrough infections with the delta variant occurs if no preventive measures are practiced. To limit infection risk, high-quality testing of participants should be considered a mandatory measure at gatherings, irrespective of the participants’ vaccination status.

Epidemiologic and Genomic Analysis of SARS-CoV-2 Delta Variant Superspreading Event in Nightclub, the Netherlands, June 2021

We report a severe acute respiratory syndrome coronavirus 2 superspreading event in the Netherlands after distancing rules were lifted in nightclubs, despite requiring a negative test or vaccination. This occurrence illustrates the potential for rapid dissemination of variants in largely unvaccinated populations under such conditions. We detected subsequent community transmission of this strain.

SARS-CoV-2 Survival in Common Non-Alcoholic and Alcoholic Beverages

SARS-CoV-2, the causative agent of COVID-19, is known to be transmitted by respiratory droplets and aerosols. Since the virus is shed at high concentrations in respiratory secretions and saliva, SARS-CoV-2 would also be expected to be transmitted through activities that involve the transfer of saliva from one individual to another, such as kissing or sharing beverages. To assess the survival of infectious SARS-CoV-2 in common beverages, we quantified infectious virus by plaque assays one hour after inoculation into 18 non-alcoholic and 16 alcoholic beverages, plus saliva, and also 7 days later for 5 of these beverages. SARS-CoV-2 remains infectious with minimal reductions in several common beverages, including milk and beer. However, cocoa, coffee, tea, fruit juices, and wine contain antiviral compounds that inactivate SARS-CoV-2. Although hard liquors containing 40% alcohol immediately inactivate SARS-CoV-2, mixing with non-alcoholic beverages reduces the antiviral effects. In summary, SARS-CoV-2 can be recovered from commonly consumed beverages in a beverage type and time-dependent manner. Although aerosol or droplet transmission remains the most likely mode of transmission, our findings combined with others suggest that beverages contaminated with SARS-CoV-2 during handling, serving, or through sharing of drinks should be considered as a potential vehicle for virus transmission.

Investigation of SARS-CoV-2 Transmission Associated With a Large Indoor Convention - New York City, November-December 2021

During November 19-21, 2021, an indoor convention (event) in New York City (NYC), was attended by approximately 53,000 persons from 52 U.S. jurisdictions and 30 foreign countries. In-person registration for the event began on November 18, 2021. The venue was equipped with high efficiency particulate air (HEPA) filtration, and attendees were required to wear a mask indoors and have documented receipt of at least 1 dose of a COVID-19 vaccine.* On December 2, 2021, the Minnesota Department of Health reported the first case of community-acquired COVID-19 in the United States caused by the SARS-CoV-2 B.1.1.529 (Omicron) variant in a person who had attended the event (1). CDC collaborated with state and local health departments to assess event-associated COVID-19 cases and potential exposures among U.S.-based attendees using data from COVID-19 surveillance systems and an anonymous online attendee survey. Among 34,541 attendees with available contact information, surveillance data identified test results for 4,560, including 119 (2.6%) persons from 16 jurisdictions with positive SARS-CoV-2 test results. Most (4,041 [95.2%]), survey respondents reported always wearing a mask while indoors at the event. Compared with test-negative respondents, test-positive respondents were more likely to report attending bars, karaoke, or nightclubs, and eating or drinking indoors near others for at least 15 minutes. Among 4,560 attendees who received testing, evidence of widespread transmission during the event was not identified. Genomic sequencing of 20 specimens identified the SARS-CoV-2 B.1.617.2 (Delta) variant (AY.25 and AY.103 sublineages) in 15 (75%) cases, and the Omicron variant (BA.1 sublineage) in five (25%) cases. These findings reinforce the importance of implementing multiple, simultaneous prevention measures, such as ensuring up-to-date vaccination, mask use, physical distancing, and improved ventilation in limiting SARS-CoV-2 transmission, during large, indoor events.†.

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.

Prediction and control of aerosol transmission of SARS-CoV-2 in ventilated context: from source to receptor

Global spread of COVID-19 has seriously threatened human life and health. The aerosol transmission route of SARS-CoV-2 is observed often associated with infection clusters under poorly ventilated environment. In the context of COVID-19 pandemic, significant transformation and optimization of traditional ventilation systems are needed. This paper is aimed to offer better understanding and insights into effective ventilation design to maximize its ability in airborne risk control, for particularly the COVID-19. Comprehensive reviews of each phase of aerosol transmission of SARS-CoV-2 from source to receptor are conducted, so as to provide a theoretical basis for risk prediction and control. Infection risk models and their key parameters for risk assessment of SARS-CoV-2 are analyzed. Special focus is given on the efficacy of different ventilation strategies in mitigating airborne transmission. Ventilation interventions are found mainly impacting on the dispersion and inhalation phases of aerosol transmission. The airflow patterns become a key factor in controlling the aerosol diffusion and distribution. Novel and personalized ventilation design, effective integration with other environmental control techniques and resilient HVAC system design to adapt both common and epidemic conditions are still remaining challenging, which need to be solved with the aid of multidisciplinary research and intelligent technologies.

Exploring the potentials of personalized ventilation in mitigating airborne infection risk for two closely ranged occupants with different risk assessment models

In the context of COVID-19, new requirements are occurring in ventilation systems to mitigate airborne transmission risk in indoor environment. Personalized ventilation (PV) which directly delivers clean air to the occupant's breathing zone is considered as a promising solution. To explore the potentials of PV in preventing the spread of infectious aerosols between closely ranged occupants, experiments were conducted with two breathing thermal manikins with three different relative orientations. Nebulized aerosols were used to mimic exhaled droplets transmitted between the occupants. Four risk assessment models were applied to evaluate the exposure or infection risk affected by PV with different operation modes. Results show that PV was effective in reducing the user's infection risk compared with mixing ventilation alone. Relative orientations and operation modes of PV significantly affected its performance in airborne risk control. The infection risk of SARS-CoV-2 was reduced by 65% with PV of 9 L/s after an exposure duration of 2 h back-to-back as assessed by the dose-response model, indicating effective protection effect of PV against airborne transmission. While the side-by-side orientation was found to be the most critical condition for PV in airborne risk control as it would accelerate diffusion of infectious droplets in lateral diffusion to occupants by side. Optimal designs of PV for closely ranged occupants were hereby discussed. The four risk assessment models were compared and validated by experiments with PV, implying basically consistent rules of the predicted risk with PV among the four models. The relevance and applicability of these models were discussed to provide a basis for risk assessment with non-uniformly distributed pathogens indoor.

Coronavirus Disease 2019: Clinics, Treatment, and Prevention

The coronavirus disease 2019 (COVID-19) pandemic, caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), emerged at the end of 2019 in China and affected the entire world population, either by infection and its health consequences, or by restrictions in daily life as a consequence of hygiene measures and containment strategies. As of September 2021, more than 231,000.000 infections and 4,740.000 deaths due to COVID-19 have been reported. The infections present with varied clinical symptoms and severity, ranging from asymptomatic course to fatal outcome. Several risk factors for a severe course of the disease have been identified, the most important being age, gender, comorbidities, lifestyle, and genetics. While most patients recover within several weeks, some report persistent symptoms restricting their daily lives and activities, termed as post-COVID. Over the past 18months, we have acquired significant knowledge as reflected by an almost uncountable number of publications on the nature of the underlying virus and its evolution, host responses to infection, modes of transmission, and different clinical presentations of the disease. Along this line, new diagnostic tests and algorithms have been developed paralleled by the search for and clinical evaluation of specific treatments for the different stages of the disease. In addition, preventive non-pharmacological measures have been implemented to control the spread of infection in the community. While an effective antiviral therapy is not yet available, numerous vaccines including novel vaccine technologies have been developed, which show high protection from infection and specifically from a severe course or death from COVID-19. In this review, we tried to provide an up-to-date schematic of COVID-19, including aspects of epidemiology, virology, clinical presentation, diagnostics, therapy, and prevention.

Decrease in overdispersed secondary transmission of COVID-19 over time in Japan

Coronavirus disease 2019 (COVID-19) has been described as having an overdispersed offspring distribution, i.e. high variation in the number of secondary transmissions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) per single primary COVID-19 case. Accordingly, countermeasures focused on high-risk settings and contact tracing could efficiently reduce secondary transmissions. However, as variants of concern with elevated transmissibility continue to emerge, controlling COVID-19 with such focused approaches has become difficult. It is vital to quantify temporal variations in the offspring distribution dispersibility. Here, we investigated offspring distributions for periods when the ancestral variant was still dominant (summer, 2020; wave 2) and when Alpha variant (B.1.1.7) was prevailing (spring, 2021; wave 4). The dispersion parameter (k) was estimated by analysing contact tracing data and fitting a negative binomial distribution to empirically observed offspring distributions from Nagano, Japan. The offspring distribution was less dispersed in wave 4 (k = 0.32; 95% confidence interval (CI) 0.24-0.43) than in wave 2 (k = 0.21 (95% CI 0.13-0.36)). A high proportion of household transmission was observed in wave 4, although the proportion of secondary transmissions generating more than five secondary cases did not vary over time. With this decreased variation, the effectiveness of risk group-focused interventions may be diminished.

Evaluation of a Rapid Antigen Test To Detect SARS-CoV-2 Infection and Identify Potentially Infectious Individuals

The identification and isolation of highly infectious SARS-CoV-2-infected individuals is an important public health strategy. Rapid antigen detection tests (RADT) are promising tools for large-scale screenings due to timely results and feasibility for on-site testing. Nonetheless, the diagnostic performance of RADT in detecting infectious individuals is not yet fully determined. In this study, RT-qPCR and virus culture of RT-qPCR-positive samples were used to evaluate and compare the performance of the Standard Q COVID-19 Ag test in detecting SARS-CoV-2-infected and possibly infectious individuals. To this end, two combined oro- and nasopharyngeal swabs were collected at a routine SARS-CoV-2 diagnostic center. A total of 2,028 samples were tested, and 118 virus cultures were inoculated. SARS-CoV-2 infection was detected in 210 samples by RT-qPCR, representing a positive rate of 10.36%. The Standard Q COVID-19 Ag test yielded a positive result in 92 (4.54%) samples resulting in an overall sensitivity and specificity of 42.86 and 99.89%, respectively. For adjusted C_T values of <20 (n = 14), <25 (n = 57), and <30 (n = 88), the RADT reached sensitivities of 100, 98.25, and 88.64%, respectively. All 29 culture-positive samples were detected by the RADT. Although the overall sensitivity was low, the Standard Q COVID-19 Ag test reliably detected patients with high RNA loads. In addition, negative RADT results fully corresponded with the lack of viral cultivability in Vero E6 cells. These results indicate that RADT can be a valuable tool for the detection of individuals with high RNA loads that are likely to transmit SARS-CoV-2.

Shared Food, Meals and Drinks: 10 Arguments Suggesting an Oral Transmission Route of SARS-CoV-2

Numerous observational, epidemiologic data have suggested that the risk of COVID19 is related to shared meals or drinks. The presence of ACE2 receptors in the gastrointestinal tract supports this hypothesis. Furthermore, several patients experience gastrointestinal symptoms without any respiratory disease. The SARS-CoV-2 found on food and packaging in China and the epidemic resurgence attributed to foods are also strong indications of an oral transmission route. Unprecedented biopersistence on skin, food, and beverages supports this theory. Finally, animal models reproducing the disease by oral inoculation are additional arguments in favor of an oro-digestive route of infection.

A comprehensive estimation of country-level basic reproduction numbers R0 for COVID-19: Regime regression can automatically estimate the end of the exponential phase in epidemic data

In a compartmental epidemic model, the initial exponential phase reflects a fixed interaction between an infectious agent and a susceptible population in steady state, so it determines the basic reproduction number R₀ on its own. After the exponential phase, dynamic complexities like societal responses muddy the practical interpretation of many estimated parameters. The computer program ARRP, already available from sequence alignment applications, automatically estimated the end of the exponential phase in COVID-19 and extracted the exponential growth rate r for 160 countries. By positing a gamma-distributed generation time, the exponential growth method then yielded R₀ estimates for COVID-19 in 160 countries. The use of ARRP ensured that the R₀ estimates were largely freed from any dependency outside the exponential phase. The Prem matrices quantify rates of effective contact for infectious disease. Without using any age-stratified COVID-19 data, but under strong assumptions about the homogeneity of susceptibility, infectiousness, etc., across different age-groups, the Prem contact matrices also yielded theoretical R₀ estimates for COVID-19 in 152 countries, generally in quantitative conflict with the R₀ estimates derived from the exponential growth method. An exploratory analysis manipulating only the Prem contact matrices reduced the conflict, suggesting that age-groups under 20 years did not promote the initial exponential growth of COVID-19 as much as other age-groups. The analysis therefore supports tentatively and tardily, but independently of age-stratified COVID-19 data, the low priority given to vaccinating younger age groups. It also supports the judicious reopening of schools. The exploratory analysis also supports the possibility of suspecting differences in epidemic spread among different age-groups, even before substantial amounts of age-stratified data become available.

Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7

BACKGROUND

International travel is a major driver of the introduction and spread of SARS-CoV-2.

AIM

To investigate SARS-CoV-2 genetic diversity in the region of a major transport hub in Germany, we characterized the viral sequence diversity of the SARS-CoV-2 variants circulating in Frankfurt am Main, the city with the largest airport in Germany, from the end of October to the end of December 2020.

METHODS

In total, we recovered 136 SARS-CoV-2 genomes from nasopharyngeal swab samples. We isolated 104 isolates that were grown in cell culture and RNA from the recovered viruses and subjected them to full-genome sequence analysis. In addition, 32 nasopharyngeal swab samples were directly sequenced.

RESULTS AND CONCLUSION

We found 28 different lineages of SARS-CoV-2 circulating during the study period, including the variant of concern B.1.1.7 (Δ69/70, N501Y). Six of the lineages had not previously been observed in Germany. We detected the spike protein (S) deletion Δ69/Δ70 in 15% of all sequences, a four base pair (bp) deletion (in 2.9% of sequences) and a single bp deletion (in 0.7% of sequences) in ORF3a, leading to ORF3a truncations. In four sequences (2.9%), an amino acid deletion at position 210 in S was identified. In a single sample (0.7%), both a 9 bp deletion in ORF1ab and a 7 bp deletion in ORF7a were identified. One sequence in lineage B.1.1.70 had an N501Y substitution while lacking the Δ69/70 in S. The high diversity of sequences observed over two months in Frankfurt am Main highlights the persisting need for continuous SARS-CoV-2 surveillance using full-genome sequencing, particularly in cities with international airport connections.

Coding-Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Gilgit, Pakistan

Here, we report the coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a nasopharyngeal swab from the first patient with COVID-19 in Gilgit, Pakistan.

Here, we report the coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a nasopharyngeal swab from the first patient with COVID-19 in Gilgit, Pakistan.

[Field investigations of SARS-CoV-2-outbreaks in Germany by the Robert Koch Institute, February-October 2020]

Das Robert Koch-Institut (RKI) bietet den Gesundheitsämtern in Deutschland bei Ausbrüchen von Infektionserkrankungen Beratung und praktische Unterstützung vor Ort an. Die Feldeinsätze werden von speziell geschultem Personal durchgeführt. Auch im Rahmen der COVID-19-Pandemie leistet das RKI regelmäßig diese Form der Amtshilfe in unterschiedlichen Settings. Dabei handelt es sich beispielsweise um Ausbrüche in Wohngebäuden, Arztpraxen, Alten- und Pflegeheimen, Kliniken, Erstaufnahmeeinrichtungen für Asylsuchende, aber auch in einem Nachtclub oder auf einem Kreuzfahrtschiff.

Der vorliegende Beitrag berichtet exemplarisch von Feldeinsätzen, die im Zeitraum Februar bis Oktober 2020 im Rahmen der COVID-19-Pandemie stattgefunden haben. Die daraus gewonnenen Erkenntnisse tragen dazu bei, das Wissen zu SARS-CoV‑2 zu erweitern, z. B. zur Übertragung und Ausbreitung des Erregers, RKI-Empfehlungen zu formulieren oder zu untermauern und das Management komplexer Situationen zu unterstützen. Die Praxisbeispiele zeigen, wie vielfältig die RKI-Teams nicht nur vor Ort unterstützen, sondern auch die epidemiologische Evidenzbasis bereichern.

Im September 2020 wurde im RKI die „Kontaktstelle für den öffentlichen Gesundheitsdienst (ÖGD)“ eingerichtet, die unter anderem die Amtshilfe durch Feldeinsätze koordiniert und erweiterte Beratungsmöglichkeiten bietet. Damit der ÖGD langfristig noch besser auf Ausbrüche von Infektionserregern reagieren kann, soll das interdisziplinäre Trainingsangebot intensiviert werden.