SARS-CoV-2 has not emerged in roe, red or fallow deer in Germany or Austria during the COVID 19 pandemic

Spillover of SARS-CoV-2 to North American white tailed deer (Odocoileus virginianus) has been documented. We evaluated pre and pandemic exposure of German and Austrian deer species using a SARS-CoV-2 pseudoneutralization assay. In stark contrast to North American white tailed deer, we found no evidence of SARS-CoV-2 exposure. Article Summary LineUsing a sensitive serological assay, 433 pre and pandemic deer samples from Germany and Austria tested negative for SARS-CoV-2-specific antibodies highlighting a major difference between central European and North American deer exposure and in their epidemiologic roles.

Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses

The furin cleavage site in SARS-CoV-2 is unique within the Severe acute respiratory syndrome-related coronavirus (SrC) species. We re-assessed diverse SrC from European horseshoe bats and reveal molecular determinants such as purine richness, RNA secondary structures and viral quasispecies potentially enabling furin cleavage. Furin cleavage thus likely emerged from the SrC bat reservoir via molecular mechanisms conserved across reservoir-bound RNA viruses, supporting a natural origin of SARS-CoV-2.

High SARS-CoV-2 seroprevalence in rural Peru, 2021; a cross-sectional population-based study

Latin America has been severely affected by the COVID-19 pandemic. The COVID-19 burden in rural settings in Latin America is unclear. We performed a cross-sectional, population-based, random-selection SARS-CoV-2 serological study during March 2021 in the rural population of San Martin region, northern Peru. The study enrolled 563 persons from 288 houses across 10 provinces, reaching 0.19% of the total rural population of San Martin. Screening for SARS-CoV-2 IgG antibodies was done using a chemiluminescence immunoassay (CLIA) and reactive sera were confirmed using a SARS-CoV-2 surrogate virus neutralization test (sVNT). Validation using pre-pandemic sera from two regions of Peru showed false-positive results in the CLIA (23/84 sera; 27%), but not in the sVNT, highlighting the pitfalls of SARS-CoV-2 antibody testing in tropical regions and the high specificity of the two-step testing algorithm. An overall 59.0% seroprevalence (95% CI: 55-63%) corroborated intense SARS-CoV-2 spread in San Martin. Seroprevalence rates between the 10 provinces varied from 41.3-74.0% (95% CI: 30-84). Higher seroprevalence was neither associated with population size, population density, surface area, mean altitude or poverty index in spearman correlations. Seroprevalence and reported incidence diverged substantially between provinces, suggesting regional biases of COVID-19 surveillance data. Potentially, limited healthcare access due to environmental, geographic, economic, and cultural factors, might lead to undetected infections in rural populations. Additionally, test avoidance to evade mandatory quarantine might affect rural regions more than urban regions. Serologic diagnostics should be pursued in resource-limited settings to inform country-level surveillance, vaccination strategies and support control measures for COVID-19. ImportanceLatin America is a global hotspot of the COVID-19 pandemic. Serological studies in Latin America have been mostly performed in urban settings. Rural populations comprise 20% of the total Latin American population. Nevertheless, information of COVID-19 spread and transmission in rural settings is scarce. Using a representative population-based seroprevalence study, we detected a high seroprevalence in rural populations in San Martin, northern Peru in 2021, reaching 41 to 74 %. However, seroprevalence and reported incidence diverged substantially between regions, suggesting either limited healthcare access or test avoidance due to mandatory quarantine. Our results suggest that rural populations are highly affected by SARS-CoV-2 even though they are socio-demographically distinct from urban populations, and that highly specific serological diagnostics should be performed in resource-limited settings to support public-health strategies of COVID-19 surveillance and control.

High efficacy of therapeutic equine hyperimmune antibodies against SARS CoV-2 variants of concern

SARS-CoV-2 variants of concern (VoC) show reduced neutralization by vaccine-induced and therapeutic monoclonal antibodies. We tested therapeutic equine polyclonal antibodies (pAbs) against four VoC (alpha, beta, epsilon and gamma). We show that equine pAbs efficiently neutralize VoC, suggesting they are an effective, broad coverage, low-cost and a scalable COVID-19 treatment.

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.

Limited specificity of SARS-CoV-2 antigen-detecting rapid diagnostic tests at low temperatures

SARS-CoV-2 antigen-detecting rapid diagnostic tests (Ag-RDTs) are available within and outside of health care settings to enable increased access to COVID-19 diagnosis. These environments include provisional testing facilities, lacking temperature control; as outside temperatures fall, recommended testing temperatures cannot be guaranteed. We report impaired specificity in two out of six Ag-RDTs when used at 2-4{degrees}C, indicating that testing in cold settings might cause false-positive results potentially entailing unwarranted quarantine assignments and incorrect incidence estimates.

Impaired performance of SARS-CoV-2 antigen-detecting rapid tests at elevated temperatures

Rapid antigen-detecting tests (Ag-RDTs) can complement molecular diagnostics for COVID-19. The recommended temperature for storage of SARS-CoV-2 Ag-RDTs ranges between 5-30{degrees}C. In many countries that would benefit from SARS-CoV-2 Ag-RDTs, mean temperatures exceed 30{degrees}C. We assessed analytical sensitivity and specificity of eleven commercially available SARS-CoV-2 Ag-RDTs using different storage and operational temperatures, including (i) long-term storage and testing at recommended conditions, (ii) recommended storage conditions followed by 10 minutes exposure to 37{degrees}C and testing at 37{degrees}C and (iii) 3 weeks storage followed by testing at 37{degrees}C. The limits of detection of SARS-CoV-2 Ag-RDTs under recommended conditions ranged from 8.2x105-7.9x107 genome copies/ml of infectious SARS-CoV-2 cell culture supernatant. Despite long-term storage at recommended conditions, 10 minutes pre-incubation of Ag-RDTs and testing at 37{degrees}C resulted in about ten-fold reduced sensitivity for 46% of SARS-CoV-2 Ag-RDTs, including both Ag-RDTs currently listed for emergency use by the World Health Organization. After 3 weeks of storage at 37{degrees}C, 73% of SARS-CoV-2 Ag-RDTs exhibited about ten-fold reduced sensitivity. Specificity of SARS-CoV-2 Ag-RDTs using cell culture-derived human coronaviruses HCoV-229E and HCoV-OC43 was not affected by storage and testing at 37{degrees}C. In summary, short- and long-term exposure to elevated temperatures likely impairs sensitivity of several SARS-CoV-2 Ag-RDTs that may translate to false-negative test results at clinically relevant virus concentrations compatible with inter-individual transmission. Ensuring appropriate transport and storage conditions, and development of tests that are more robust across temperature fluctuations will be important for accurate use of SARS-CoV-2 Ag-RDTs in tropical settings.

SARS-CoV-2 Genomic Surveillance in Costa Rica: Evidence of a Divergent Population and an Increased Detection of a Spike T1117I Mutation

Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. Costa Rica was first exemplary for the region in its pandemic control, declaring a swift state of emergency on March 16th that led to a low quantity of cases, until measures were lifted in early May. From the first detected case in March 6th to December 31st almost 170 000 cases have been reported in Costa Rica, 99.5% of them from May onwards. We analyzed the genomic variability during the SARS-CoV-2 pandemic in Costa Rica using 185 sequences, 52 from the first months of the pandemic, and 133 from the current wave. Three GISAID clades (G, GH, and GR) and three PANGOLIN lineages (B.1, B.1.1, and B.1.291) are predominant, with phylogenetic relationships that are in line with the results of other Latin American countries, suggesting introduction and multiple re-introductions from other regions of the world. The whole-genome variant calling analysis identified a total of 283 distinct nucleotide variants. These correspond mostly to non-synonymous mutations (51.6%, 146) but 45.6% (129) corresponded to synonymous mutations. The 283 variants showed an expected power-law distribution: 190 single nucleotide mutations were identified in single sequences, only 16 single nucleotide mutations were found in >5% sequences, and only two mutations in >50% genomes. These mutations were distributed through the whole genome. However, 63.6% were present in ORF1ab, 11.7% in Spike gene and 10.6% in the Nucleocapsid gene. Additionally, the prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere. Interestingly, the frequency of mutation T1117I in the Spike has increased during the current pandemic wave beginning in May 2020 in Costa Rica, reaching 29.2% detection in the full genome analyses in November 2020. This variant has been observed in less than 1% of the GISAID reported sequences worldwide in all the 2020. Structural modeling of the Spike protein with the T1117I mutation suggest a potential effect on the viral oligomerization needed for cell infection, but no differences with other genomes on transmissibility, severity nor vaccine effectiveness are predicted. Nevertheless, in-vitro experiments are required to support these in-silico findings. In conclusion, genome analyses of the SARS-CoV-2 sequences over the course of COVID-19 pandemic in Costa Rica suggest introduction of lineages from other countries as travel bans and measures were lifted, similar to results found in other studies, as well as an increase in the Spike-T1117I variant that needs to be monitored and studied in further analyses as part of the surveillance program during the pandemic.

Comparison of seven commercial SARS-CoV-2 rapid Point-of-Care Antigen tests

BackgroundAntigen point of care tests (AgPOCT) can accelerate SARS-CoV-2 testing. As first AgPOCT are becoming available, there is a growing interest in their utility and performance. MethodsHere we compare AgPOCT products by seven suppliers: the Abbott Panbio COVID-19 Ag Rapid Test; the RapiGEN BIOCREDIT COVID-19 Ag; the Healgen(R) Coronavirus Ag Rapid Test Cassette (Swab); the Coris Bioconcept Covid.19 Ag Respi-Strip; the R-Biopharm RIDA(R)QUICK SARS-CoV-2 Antigen; the NAL von minden NADAL COVID19-Ag Test; and the Roche/SD Biosensor SARS-CoV Rapid Antigen Test. Tests were evaluated on recombinant nucleoprotein, cultured endemic and emerging coronaviruses, stored clinical samples with known SARS-CoV-2 viral loads (n=138), stored samples from patients with respiratory agents other than SARS-CoV-2 (n=100), as well as self-sampled swabs from healthy volunteers (n=35). FindingsLimits of detection in six of seven tested products ranged between 2.08 x 106 and 2.88 x 107 copies per swab, the outlier at 1.58 x 1010 copies per swab. Specificities ranged between 98.53% and 100% in five products, with two outliers at 94.85% and 88.24%. False positive results were not associated with any specific respiratory agent. As some of the tested AgPOCT were early production lots, the observed issues with specificity are unlikely to persist. InterpretationThe sensitivity range of most AgPOCT overlaps with viral load figures typically observed during the first week of symptoms, which marks the infectious period in the majority patients. AgPOCTs with a limit of detection that approximates the virus concentration above which patients are infectious may enable shortcuts in decision-making in various areas of healthcare and public health.

Diagnostics and spread of SARS-CoV-2 in Western Africa: An observational laboratory-based study from Benin

Information on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spread in Africa is limited by fragile surveillance systems and insufficient diagnostic capacity. We assessed the coronavirus disease-19 (COVID-19)-related diagnostic workload in Benin, Western Africa, characterized SARS-CoV-2 genomes from 12 acute cases of COVID-19, used those together with public data to estimate SARS-CoV-2 transmission dynamics in a Bayesian framework, validated a widely used diagnostic dual target RT-PCR kit donated to African countries, and conducted serological analyses in 68 sera from confirmed COVID-19 cases and from febrile patients sampled before the predicted SARS-CoV-2 introduction. We found a 15-fold increase in the monthly laboratory workload due to COVID-19. Genomic surveillance showed introductions of three distinct SARS-CoV-2 lineages. SARS-CoV-2 genome-based analyses yielded an R0 estimate of 4.4 (95% confidence interval: 2.0-7.7), suggesting intense spread of SARS-CoV-2 in Africa. RT-PCR-based tests were highly sensitive but showed variation of internal controls and between diagnostic targets. Commercially available SARS-CoV-2 ELISAs showed up to 25% false-positive results depending on antigen and antibody types, likely due to unspecific antibody responses elicited by acute malaria according to lack of SARS-CoV-2-specific neutralizing antibody responses and relatively higher parasitemia in those sera. We confirm an overload of the diagnostic capacity in Benin and provide baseline information on the usability of genome-based surveillance in resource-limited settings. Sero-epidemiological studies needed to assess SARS-CoV-2 spread may be put at stake by low specificity of tests in tropical settings globally. The increasing diagnostic challenges demand continuous support of national and supranational African stakeholders. FundingThis work was supported by the Deutsche Gesellschaft fur Internationale Zusammenarbeit (GIZ) GmbH.