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1.
Clin Infect Dis ; 2022 Jun 25.
Article in English | MEDLINE | ID: covidwho-1908772

ABSTRACT

BACKGROUND: Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other SARS-CoV-2 variants of concern led to an expansion of genomic sequencing activities in Germany. METHODS: At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the "Integrated Molecular Surveillance for SARS-CoV-2" (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2 positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI. RESULTS: We report analyses of 3,623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3,282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modelled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave. CONCLUSIONS: SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling COVID-19 spread as the virus evolves.

2.
Influenza Other Respir Viruses ; 16(5): 854-857, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1822050

ABSTRACT

Based on our national outpatient sentinel surveillance, we have developed a novel approach to determine respiratory syncytial virus (RSV) epidemic seasons in Germany by using RSV positivity rate and its lower limit of 95% confidence interval. This method was evaluated retrospectively on nine RSV seasons, and it is also well-suited to describe off-season circulation of RSV in near real time as observed for seasons 2020/21 and 2021/22 during the COVID-19 pandemic. Prospective application is of crucial importance to enable timely actions for health service delivery and prevention.


Subject(s)
Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , COVID-19 , Confidence Intervals , Germany/epidemiology , Humans , Infant , Pandemics , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus, Human/genetics , Retrospective Studies , Seasons
3.
Microorganisms ; 9(7)2021 Jul 14.
Article in English | MEDLINE | ID: covidwho-1323308

ABSTRACT

Human parainfluenza viruses (HPIVs) are important causes of respiratory illness, especially in young children. However, surveillance for HPIV is rarely performed continuously, and national-level epidemiologic and genetic data are scarce. Within the German sentinel system, to monitor acute respiratory infections (ARI), 4463 respiratory specimens collected from outpatients < 5 years of age between October 2015 and September 2019 were retrospectively screened for HPIV 1-4 using real-time PCR. HPIV was identified in 459 (10%) samples. HPIV-3 was the most common HPIV-type, with 234 detections, followed by HPIV-1 (113), HPIV-4 (61), and HPIV-2 (49). HPIV-3 was more frequently associated with age < 2 years, and HPIV-4 was more frequently associated with pneumonia compared to other HPIV types. HPIV circulation displayed distinct seasonal patterns, which appeared to vary by type. Phylogenetic characterization clustered HPIV-1 in Clades 2 and 3. Reclassification was performed for HPIV-2, provisionally assigning two distinct HPIV-2 groups and six clades, with German HPIV-2s clustering in Clade 2.4. HPIV-3 clustered in C1, C3, C5, and, interestingly, in A. HPIV-4 clustered in Clades 2.1 and 2.2. The results of this study may serve to inform future approaches to diagnose and prevent HPIV infections, which contribute substantially to ARI in young children in Germany.

4.
Lancet Reg Health Eur ; 6: 100112, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1260816

ABSTRACT

BACKGROUND: During the initial COVID-19 response, Germany's Federal Government implemented several nonpharmaceutical interventions (NPIs) that were instrumental in suppressing early exponential spread of SARS-CoV-2. NPI effect on the transmission of other respiratory viruses has not been examined at the national level thus far. METHODS: Upper respiratory tract specimens from 3580 patients with acute respiratory infection (ARI), collected within the nationwide German ARI Sentinel, underwent RT-PCR diagnostics for multiple respiratory viruses. The observation period (weeks 1-38 of 2020) included the time before, during and after a far-reaching contact ban. Detection rates for different viruses were compared to 2017-2019 sentinel data (15350 samples; week 1-38, 11823 samples). FINDINGS: The March 2020 contact ban, which was followed by a mask mandate, was associated with an unprecedented and sustained decline of multiple respiratory viruses. Among these, rhinovirus was the single agent that resurged to levels equalling those of previous years. Rhinovirus rebound was first observed in children, after schools and daycares had reopened. By contrast, other nonenveloped viruses (i.e. gastroenteritis viruses reported at the national level) suppressed after the shutdown did not rebound. INTERPRETATION: Contact restrictions with a subsequent mask mandate in spring may substantially reduce respiratory virus circulation. This reduction appears sustained for most viruses, indicating that the activity of influenza and other respiratory viruses during the subsequent winter season might be low,whereas rhinovirus resurgence, potentially driven by transmission in educational institutions in a setting of waning population immunity, might signal predominance of rhinovirus-related ARIs. FUNDING: Robert Koch-Institute and German Ministry of Health.

5.
J Clin Microbiol ; 59(3)2021 02 18.
Article in English | MEDLINE | ID: covidwho-1125060

ABSTRACT

During the ongoing coronavirus disease 2019 (COVID-19) outbreak, robust detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key element for clinical management and to interrupt transmission chains. We organized an external quality assessment (EQA) of molecular detection of SARS-CoV-2 for European expert laboratories. An EQA panel composed of 12 samples, containing either SARS-CoV-2 at different concentrations to evaluate sensitivity or other respiratory viruses to evaluate specificity of SARS-CoV-2 testing, was distributed to 68 laboratories in 35 countries. Specificity samples included seasonal human coronaviruses hCoV-229E, hCoV-NL63, and hCoV-OC43, as well as Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, and human influenza viruses A and B. Sensitivity results differed among laboratories, particularly for low-concentration SARS-CoV-2 samples. Results indicated that performance was mostly independent of the selection of specific extraction or PCR methods.


Subject(s)
COVID-19 Testing/standards , COVID-19/diagnosis , Coronavirus 229E, Human , Coronavirus NL63, Human , Coronavirus OC43, Human , Humans , Influenzavirus A , Influenzavirus B , Laboratories , Middle East Respiratory Syndrome Coronavirus , SARS Virus , SARS-CoV-2 , Sensitivity and Specificity
6.
J Clin Microbiol ; 59(3)2021 02 18.
Article in English | MEDLINE | ID: covidwho-966598

ABSTRACT

During the ongoing coronavirus disease 2019 (COVID-19) outbreak, robust detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key element for clinical management and to interrupt transmission chains. We organized an external quality assessment (EQA) of molecular detection of SARS-CoV-2 for European expert laboratories. An EQA panel composed of 12 samples, containing either SARS-CoV-2 at different concentrations to evaluate sensitivity or other respiratory viruses to evaluate specificity of SARS-CoV-2 testing, was distributed to 68 laboratories in 35 countries. Specificity samples included seasonal human coronaviruses hCoV-229E, hCoV-NL63, and hCoV-OC43, as well as Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, and human influenza viruses A and B. Sensitivity results differed among laboratories, particularly for low-concentration SARS-CoV-2 samples. Results indicated that performance was mostly independent of the selection of specific extraction or PCR methods.


Subject(s)
COVID-19 Testing/standards , COVID-19/diagnosis , Coronavirus 229E, Human , Coronavirus NL63, Human , Coronavirus OC43, Human , Humans , Influenzavirus A , Influenzavirus B , Laboratories , Middle East Respiratory Syndrome Coronavirus , SARS Virus , SARS-CoV-2 , Sensitivity and Specificity
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