Detection of Enterovirus D68 in Wastewater Samples from the UK between July and November 2021

Infection with enterovirus D68 (EV-D68) has been linked with severe neurological disease such as acute flaccid myelitis (AFM) in recent years. However, active surveillance for EV-D68 is lacking, which makes full assessment of this association difficult. Although a high number of EV-D68 infections were expected in 2020 based on the EV-D68′s known biannual circulation patterns, no apparent increase in EV-D68 detections or AFM cases was observed during 2020. We describe an upsurge of EV-D68 detections in wastewater samples from the United Kingdom between July and November 2021 mirroring the recently reported rise in EV-D68 detections in clinical samples from various European countries. We provide the first publicly available 2021 EV-D68 sequences showing co-circulation of EV-D68 strains from genetic clade D and sub-clade B3 as in previous years. Our results show the value of environmental surveillance (ES) for the early detection of circulating and clinically relevant human viruses. The use of a next-generation sequencing (NGS) approach helped us to estimate the prevalence of EV-D68 viruses among EV strains from other EV serotypes and to detect EV-D68 minor variants. The utility of ES at reducing gaps in virus surveillance for EV-D68 and the possible impact of nonpharmaceutical interventions introduced to control the COVID-19 pandemic on EV-D68 transmission dynamics are discussed.

An Outbreak in Pigeons Caused by the Subgenotype VI.2.1.2 of Newcastle Disease Virus in Brazil

Newcastle disease virus (NDV) can infect over 250 bird species with variable pathogenicity; it can also infect humans in rare cases. The present study investigated an outbreak in feral pigeons in São Paulo city, Brazil, in 2019. Affected birds displayed neurological signs, and hemorrhages were observed in different tissues. Histopathology changes with infiltration of mononuclear inflammatory cells were also found in the brain, kidney, proventriculus, heart, and spleen. NDV staining was detected by immunohistochemistry. Twenty-seven out of thirty-four tested samples (swabs and tissues) were positive for Newcastle disease virus by RT-qPCR test, targeting the M gene. One isolate, obtained from a pool of positive swab samples, was characterized by the intracerebral pathogenicity index (ICPI) and the hemagglutination inhibition (HI) tests. This isolate had an ICPI of 0.99, confirming a virulent NDV strain. The monoclonal antibody 617/161, which recognizes a distinct epitope in pigeon NDV strains, inhibited the isolate with an HI titer of 512. A complete genome of NDV was obtained using next-generation sequencing. Phylogenetic analysis based on the complete CDS F gene grouped the detected isolate with other viruses from subgenotype VI.2.1.2, class II, including one previously reported in Southern Brazil in 2014. This study reports a comprehensive characterization of the subgenotype VI.2.1.2, which seems to have been circulating in Brazilian urban areas since 2014. Due to the zoonotic risk of NDV, virus surveillance in feral pigeons should also be systematically performed in urban areas.

Mosquito excreta reveals circulation of West Nile virus and its underlying ecosystem

Emerging and endemic mosquito-borne viruses can be difficult to detect and monitor because they often cause asymptomatic infections in human or vertebrate animals or cause nonspecific febrile illness with a short recovery waiting period. Cases’ detection in vertebrate hosts can be complemented by entomological surveillance, but this method is not adapted to low infection rates in mosquito populations that typically occur in low or non-endemic areas. We identified West Nile Virus circulation in Camargue, a wetland area in South of France, using a cost effective innovative xenomonitoring method based on the molecular detection of virus in excreta from trapped mosquitoes. We also succeeded at identifying the mosquito community diversity dynamic on several sampling sites, together with the vertebrate hosts on which they fed prior to be captured using amplicon-based metagenomic on mosquito excreta without processing any mosquito. Mosquito excreta-based virus surveillance can be considered as a cost-effective and non-invasive strategy that offers the additional asset to reveal the ecological network underlying arbovirus circulation.

The Power of Computational Intelligence Methods in the Containment of COVID-19 Pandemic from Detection to Recovery

The coronavirus disease (SARS-CoV-2)) pandemic has caused unprecedented economic crises, and changes in our lifestyle to different things that we have not experienced before in this century, which cause by movement restriction order by the authority to halt the spread of the disease around the globe. Researchers around the globe applied computational intelligence methods in numerous fields which exhibits a successful story. The computational intelligence methods play an important role in dealing with coronavirus pandemics. This research will focus on the use of computational intelligence methods in understanding the infection, accelerating drugs and treatments research, detecting, diagnosis, and predicting the virus, surveillance, and contact tracing to prevent or slow the virus from the spread, monitoring the recovery of the infected individuals. This study points out promising CI techniques utilized as an adjunct along with the current methods used in containments of COVID-19. It is imagined that this study will give CI researchers and the wider community an outline of the current status of CI applications and motivate CI researchers in harnessing CI technique possibilities in the battle against COVID-19.

1331. Seasonality of Common Human Coronaviruses in the United States, 2014-2021

Background The four common human coronavirus (HCoV) types, including two alpha (NL63 and 229E) and two beta (HKU1 and OC43) coronaviruses, generally cause mild, upper respiratory illness. Common HCoV seroprevalence increases rapidly during the first five years of life and remains high throughout adulthood. HCoVs are known to have seasonal patterns, with variation in predominant types each year, but more defined measures of seasonality are needed. Methods We describe laboratory detection, percent positivity, and seasonality of the four common HCoVs during July 2014 to May 2021 in the United States reported to the National Respiratory and Enteric Virus Surveillance System (NREVSS). We also describe age, sex, and co-detection with other respiratory viruses for a subset of specimens available through the Public Health Laboratory Interoperability Project (PHLIP). We used a method previously validated for respiratory syncytial virus, characterized by a centered 5-week moving average and normalization to peak, to define seasonal inflections, including season onset, peak, and offset. Results Any HCoV type was detected in 96,336 (3.4%) of 2,487,736 specimens. Predominant common HCoV types fluctuated by surveillance year (Figure 1) and were generally consistent across geographic regions. In a subset of 4,576 specimens with a common HCoV detection, those with type 229E had a higher median age compared to other HCoV types (30.8 versus 24.8 years, p< 0.001), but there were no differences by sex. Influenza was the most commonly co-detected virus. In the last six complete HCoV seasons, onsets ranged from October to November, peaks from January to February, and offsets from April to June; >95% of all HCoV detections occurred within these ranges. The 2020-2021 common HCoV season onset, dominated by types NL63 and OC43, was delayed by approximately two months compared to prior seasons. Figure 1. The top panel represents total specimens tested and the bottom panel shows percent positivity of the four common human coronavirus (HCoV) types by week starting July 5, 2014 through May 8, 2021. Data are from the National Respiratory and Enteric Virus Surveillance System (NREVSS). Conclusion Common HCoVs demonstrate relatively consistent seasonal patterns. The delayed onset of the 2020-2021 season may be attributable to mitigation measures implemented across the US including masking, improved hand hygiene, and social distancing. Better defining HCoV seasonality can inform clinical preparedness and testing practices and may provide insights into the behavior of emerging coronaviruses. Disclosures All Authors: No reported disclosures

Zika virus endemic challenges during COVID-19 pandemic in Africa

Zika virus remains endemic and opportunistic of high transmission in the tropical region of Africa, and the repeated cases of the Zika virus in Africa made it public health emergency in 2016. Amidst the COVID-19 pandemic, the catastrophic cases of unknown and unreported deaths overwhelming the region of Africa could not give health attention to respond to other endemic diseases. Here, we present the possible complication and challenges associated with the Zika virus in Africa and COVID-19 predominance, shifting the attention from the Zika virus surveillance. This paper determines to enlighten the reader about the situation, the efforts to curb the transmission of both the Zika virus and the COVID-19 pandemic. Therefore, the report recommends sustainable solutions that can lessen the threat to public health.

Identifying and prioritizing potential human-infecting viruses from their genome sequences

Determining which animal viruses may be capable of infecting humans is currently intractable at the time of their discovery, precluding prioritization of high-risk viruses for early investigation and outbreak preparedness. Given the increasing use of genomics in virus discovery and the otherwise sparse knowledge of the biology of newly discovered viruses, we developed machine learning models that identify candidate zoonoses solely using signatures of host range encoded in viral genomes. Within a dataset of 861 viral species with known zoonotic status, our approach outperformed models based on the phylogenetic relatedness of viruses to known human-infecting viruses (area under the receiver operating characteristic curve [AUC] = 0.773), distinguishing high-risk viruses within families that contain a minority of human-infecting species and identifying putatively undetected or so far unrealized zoonoses. Analyses of the underpinnings of model predictions suggested the existence of generalizable features of viral genomes that are independent of virus taxonomic relationships and that may preadapt viruses to infect humans. Our model reduced a second set of 645 animal-associated viruses that were excluded from training to 272 high and 41 very high-risk candidate zoonoses and showed significantly elevated predicted zoonotic risk in viruses from nonhuman primates, but not other mammalian or avian host groups. A second application showed that our models could have identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a relatively high-risk coronavirus strain and that this prediction required no prior knowledge of zoonotic Severe Acute Respiratory Syndrome (SARS)-related coronaviruses. Genome-based zoonotic risk assessment provides a rapid, low-cost approach to enable evidence-driven virus surveillance and increases the feasibility of downstream biological and ecological characterization of viruses.

In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2

Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. Using high throughput sequencing, we identified a single mutation in RNA-dependent RNA polymerase (NSP12) at a residue conserved among all coronaviruses in two independently evolved populations displaying decreased RDV sensitivity. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. Substitution of E802 did not affect viral replication or activity of an alternate nucleoside analogue (EIDD2801) but did affect virus fitness in a competition assay. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we observed an excess of substitutions in spike at corresponding sites identified in the emerging SARS-CoV-2 variants of concern (i.e., H69, E484, N501, H655) indicating that they can arise in vitro in the absence of immune selection. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance.