Biases in COVID-19 Case and Death Definitions: Potential Causes and Consequences.

This paper investigates three controversies involving potential causes and consequences of information bias in case and death definitions during the coronavirus disease (COVID-19) pandemic. First, evidence suggests China's surveillance data were biased and misinterpreted by the World Health Organization (WHO), prompting the WHO to advise nations to copy China's lockdowns. China appeared to use narrow diagnostic definitions that undercounted cases and deaths. Second, novel genomic data disseminated during the pandemic without adequate guidance from rigorous epidemiologic studies biased infection control policies in many countries. A novel genomic sequence of a virus is insufficient to declare new cases of a novel disease. Third, media reports of COVID-19 surveillance data in many nations appeared to be biased. Broadened surveillance definitions captured additional information, but unadjusted surveillance data disseminated to the public are not true cases and deaths. Recommendations include clarification of the proper use of diagnostic and surveillance case and death definitions to avoid information bias.

Occurrence and transport of SARS-CoV-2 in wastewater streams and its detection and remediation by chemical-biological methods.

This paper explains the transmission of SARS-CoV and influences of several environmental factors in the transmission process. The article highlighted several methods of collection, sampling and monitoring/estimation as well as surveillance tool for detecting SARS-CoV in wastewater streams. In this context, WBE (Wastewater based epidemiology) is found to be the most effective surveillance tool. Several methods of genomic sequencing are discussed in the paper, which are applied in WBE, like qPCR-based wastewater testing, metagenomics-based analysis, next generation sequencing etc. Additionally, several types of biosensors (colorimetric biosensor, mobile phone-based biosensors, and nanomaterials-based biosensors) showed promising results in sensing SARS-CoV in wastewater. Further, this review paper outlined the gaps in assessing the factors responsible for transmission and challenges in detection and monitoring along with the remediation and disinfection methods of this virus in wastewater. Various methods of disinfection of SARS-CoV-2 in wastewater are discussed (primary, secondary, and tertiary phases) and it is found that a suite of disinfection methods can be used for complete disinfection/removal of the virus. Application of ultraviolet light, ozone and chlorine-based disinfectants are also discussed in the context of treatment methods. This study calls for continuous efforts to gather more information about the virus through continuous monitoring and analyses and to address the existing gaps and identification of the most effective tool/ strategy to prevent SARS-CoV-2 transmission. Wastewater surveillance can be very useful in effective surveillance of future pandemics and epidemics caused by viruses, especially after development of new technologies in detecting and disinfecting viral pathogens more effectively.

The TeleKidSeq pilot study: incorporating telehealth into clinical care of children from diverse backgrounds undergoing whole genome sequencing.

BACKGROUND: The COVID-19 pandemic forced healthcare institutions and many clinical research programs to adopt telehealth modalities in order to mitigate viral spread. With the expanded use of telehealth, there is the potential to increase access to genomic medicine to medically underserved populations, yet little is known about how best to communicate genomic results via telehealth while also ensuring equitable access. NYCKidSeq, a multi-institutional clinical genomics research program in New York City, launched the TeleKidSeq pilot study to assess alternative forms of genomic communication and telehealth service delivery models with families from medically underserved populations. METHODS: We aim to enroll 496 participants between 0 and 21 years old to receive clinical genome sequencing. These individuals have a neurologic, cardiovascular, and/or immunologic disease. Participants will be English- or Spanish-speaking and predominantly from underrepresented groups who receive care in the New York metropolitan area. Prior to enrollment, participants will be randomized to either genetic counseling via videoconferencing with screen-sharing or genetic counseling via videoconferencing without screen-sharing. Using surveys administered at baseline, results disclosure, and 6-months post-results disclosure, we will evaluate the impact of the use of screen-sharing on participant understanding, satisfaction, and uptake of medical recommendations, as well as the psychological and socioeconomic implications of obtaining genome sequencing. Clinical utility, cost, and diagnostic yield of genome sequencing will also be assessed. DISCUSSION: The TeleKidSeq pilot study will contribute to innovations in communicating genomic test results to diverse populations through telehealth technology. In conjunction with NYCKidSeq, this work will inform best practices for the implementation of genomic medicine in diverse, English- and Spanish-speaking populations.

FAST: FPGA-based Acceleration of Genomic Sequence Trimming

The sheer amount of genomic sequencing data generated daily that requires time-sensitive processing for downstream analysis calls for accelerating the bioinformatics pipelines. Previous studies mainly have attempted accelerating the alignment stage, leaving the other pipeline stages as performance bottlenecks. In this work, we propose the first FPGA-based framework dubbed FAST to accelerate the stages that deal with sequence trimming, in particular adapter and primer removal. FAST supports a comprehensive set of functionalities and is convenient to use by operating on standard genomics data formats. The proposed framework is fully configurable and supports variety of runtime settings. It surpasses the state-of-the-art widely-used adapter trimmer (fastp) by 4.7×-29.4× speed-up, with 10.1×-54.9 less energy, respectively. For clipping primers, which with current existing tool (iVar) accounts for ∼50% of SARS-CoV-2 analysis pipeline, FAST achieves up to 62× speed-up in trimming the virus sequences with a low FPGA resource utilization of 12%. © 2022 IEEE.

Opening up safely: public health system requirements for ongoing COVID-19 management based on evaluation of Australia's surveillance system performance.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) community transmission was eliminated in Australia from 1/11/2020 to 30/6/2021, allowing evaluation of surveillance system performance in detecting novel outbreaks, including against variants of concern (VoCs). This paper aims to define system requirements for coronavirus disease 2019 (COVID-19) surveillance under future transmission and response scenarios, based on surveillance system performance to date. METHODS: This study described and evaluated surveillance systems and epidemiological characteristics of novel outbreaks based on publicly available data, and assessed surveillance system sensitivity and timeliness in outbreak detection. These findings were integrated with analysis of other critical COVID-19 public health measures to establish future COVID-19 management requirements. RESULTS: Twenty-five epidemiologically distinct outbreaks and five distinct clusters were identified in the study period, all linked through genomic sequencing to novel introductions from international travellers. Seventy percent (21/30) were detected through community testing of people with acute respiratory illness, and 30% (9/30) through quarantine screening. On average, 2.07% of the State population was tested in the week preceding detection for those identified through community surveillance. From 17/30 with publicly available data, the average time from seeding to detection was 4.9 days. One outbreak was preceded by unexpected positive wastewater results. Twenty of the 24 outbreaks in 2021 had publicly available sequencing data, all of which identified VoCs. A surveillance strategy for future VoCs similar to that used for detecting SARS-CoV-2 would require a 100-1000-fold increase in genomic sequencing capacity compared to the study period. Other essential requirements are maintaining outbreak response capacity and developing capacity to rapidly engineer, manufacture, and distribute variant vaccines at scale. CONCLUSIONS: Australia's surveillance systems performed well in detecting novel introduction of SARS-CoV-2 while community transmission was eliminated; introductions were infrequent and case numbers were low. Detection relied on quarantine screening and community surveillance in symptomatic members of the general population, supported by comprehensive genomic sequencing. Once vaccine coverage is maximised, future COVID-19 control should shift to detection of SARS-CoV-2 VoCs, requiring maintenance of surveillance systems and testing all international arrivals, alongside greatly increased genomic sequencing capacity. Effective government support of localised public health response mechanisms and engagement of all sectors of the community is crucial to current and future COVID-19 management.

Sierra SARS-CoV-2 sequence and antiviral resistance analysis program.

INTRODUCTION: Although most laboratories are capable of employing established protocols to perform full-genome SARS-CoV-2 sequencing, many are unable to assess sequence quality, select appropriate mutation-detection thresholds, or report on the potential clinical significance of mutations in the targets of antiviral therapy METHODS: We describe the technical aspects and benchmark the performance of Sierra SARS-CoV-2, a program designed to perform these functions on user-submitted FASTQ and FASTA sequence files and lists of Spike mutations. Sierra SARS-CoV-2 indicates which sequences contain an unexpectedly large number of unusual mutations and which mutations are associated with reduced susceptibility to clinical stage mAbs, the RdRP inhibitor remdesivir, or the Mpro inhibitor nirmatrelvir RESULTS: To assess the performance of Sierra SARS-CoV-2 on FASTQ files, we applied it to 600 representative FASTQ sequences and compared the results to the COVID-19 EDGE program. To assess its performance on FASTA files, we applied it to nearly one million representative FASTA sequences and compared the results to the GISAID mutation annotation. To assess its performance on mutations lists, we applied it to 13,578 distinct Spike RBD mutation patterns and showed that exactly or partially matching annotations were available for 88% of patterns CONCLUSION: Sierra SARS-CoV-2 leverages previously published data to improve the quality control of submitted viral genomic data and to provide functional annotation on the impact of mutations in the targets of antiviral SARS-CoV-2 therapy. The program can be found at https://covdb.stanford.edu/sierra/sars2/ and its source code at https://github.com/hivdb/sierra-sars2.

Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns.

Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM ("intrahost SARS-CoV-2 k-mer identification method") to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.

Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.

BACKGROUND: Universities are vulnerable to infectious disease outbreaks, making them ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures. Here, we analyze multimodal COVID-19-associated data collected during the 2020-2021 academic year at Colorado Mesa University and introduce a SARS-CoV-2 surveillance and response framework. METHODS: We analyzed epidemiological and sociobehavioral data (demographics, contact tracing, and WiFi-based co-location data) alongside pathogen surveillance data (wastewater and diagnostic testing, and viral genomic sequencing of wastewater and clinical specimens) to characterize outbreak dynamics and inform policy. We applied relative risk, multiple linear regression, and social network assortativity to identify attributes or behaviors associated with contracting SARS-CoV-2. To characterize SARS-CoV-2 transmission, we used viral sequencing, phylogenomic tools, and functional assays. FINDINGS: Athletes, particularly those on high-contact teams, had the highest risk of testing positive. On average, individuals who tested positive had more contacts and longer interaction durations than individuals who never tested positive. The distribution of contacts per individual was overdispersed, although not as overdispersed as the distribution of phylogenomic descendants. Corroboration via technical replicates was essential for identification of wastewater mutations. CONCLUSIONS: Based on our findings, we formulate a framework that combines tools into an integrated disease surveillance program that can be implemented in other congregate settings with limited resources. FUNDING: This work was supported by the National Science Foundation, the Hertz Foundation, the National Institutes of Health, the Centers for Disease Control and Prevention, the Massachusetts Consortium on Pathogen Readiness, the Howard Hughes Medical Institute, the Flu Lab, and the Audacious Project.

Genomic characterisation reveals a dominant lineage of SARS-CoV-2 in Papua New Guinea.

The coronavirus disease pandemic has highlighted the utility of pathogen genomics as a key part of comprehensive public health response to emerging infectious diseases threats, however, the ability to generate, analyse, and respond to pathogen genomic data varies around the world. Papua New Guinea (PNG), which has limited in-country capacity for genomics, has experienced significant outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with initial genomics data indicating a large proportion of cases were from lineages that are not well defined within the current nomenclature. Through a partnership between in-country public health agencies and academic organisations, industry, and a public health genomics reference laboratory in Australia a system for routine SARS-CoV-2 genomics from PNG was established. Here we aim to characterise and describe the genomics of PNG's second wave and examine the sudden expansion of a lineage that is not well defined but very prevalent in the Western Pacific region. We generated 1797 sequences from cases in PNG and performed phylogenetic and phylodynamic analyses to examine the outbreak and characterise the circulating lineages and clusters present. Our results reveal the rapid expansion of the B.1.466.2 and related lineages within PNG, from multiple introductions into the country. We also highlight the difficulties that unstable lineage assignment causes when using genomics to assist with rapid cluster definitions.

Detection of SARS-CoV-2 Variants of Concern with Tiling Amplicon Sequencing from Wastewater

The emerging variants of concern (VOCs) of SARS-CoV-2, e.g., Alpha, Beta, Gamma, Delta, and Omicron, have constrained the global response to the COVID-19 pandemic. They challenge our current capability to identify and distinguish variants from wastewater, due to the high likelihood of viral RNA degradation and the prior knowledge required for primer design. This study focused on the detection of multiple VOCs of SARS-CoV-2 using a high-throughput, multiplexed, amplicon-based sequencing technology, namely, ATOPlex. We first demonstrated that this method can discern multiple variants from artificial samples consisting of four synthetic strains of SARS-CoV-2. The ability of ATOPlex to identify VOCs was further validated using real wastewater samples collected from both an international passenger flight and local wastewater treatment plants. On the basis of phylogenetic analysis and the identification of single-nucleotide polymorphism on the genomes, the ATOPlex method was shown to be effective in detecting three VOCs, including two Beta variants and one Delta variant from either local wastewater or flight sewage samples, which were phylogenetically close to the variants that originated from France, Philippines, and the United States. We found this method is mutation-independent, rendering it a tool for proactive detection of SARS-CoV-2 VOCs in wastewater for the application of wastewater-based epidemiology.

Erratum: Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka.

[This corrects the article DOI: 10.3389/fmicb.2021.722838.].

Previous SARS-CoV-2 Infection Status Among the Current RT-PCR-Positive Individuals Affected During the Second Wave of COVID-19 Infections in Chennai, India.

India witnessed a very strong second wave of coronavirus disease 2019 (COVID-19) during March and June 2021. Newly emerging variants of concern can escape immunity and cause reinfection. We tested newly diagnosed COVID-19 cases during the second wave in Chennai, India for the presence of Immunoglobulin G (IgG) antibodies to estimate the extent of re-infection. Of the 902 unvaccinated COVID-19 positive individuals, 53 (26.5%) were reactive for IgG antibodies and non-reactive for Immunogobulin M (IgM) antibodies. Among the 53 IgG-positive individuals, the interval between symptom onset (or last contact with the known case in case of asymptomatic) was <5 days in 29 individuals, ≥5 days in 11 individuals, while 13 asymptomatic individuals did not know their last contact with a positive case. The possible re-infections ranged between 3.2% (95% CI: 2.2-4.5%) and 4.3% (95% CI: 3.4-6.2%). The findings indicate that re-infection was not a major reason of the surge in cases during second wave. The IgG seropositivity among recently diagnosed unvaccinated COVID-19 patients could provide early indications about the extent of re-infections in the area.

A pilot of Blood-First diagnostic cell free DNA (cfDNA) next generation sequencing (NGS) in patients with suspected advanced lung cancer.

INTRODUCTION: The diagnostic pathway for lung cancer can be long. Availability of front-line targeted therapies for NSCLC demands access to good quality tissue for genomic sequencing and rapid reporting of results. Diagnosis of lung cancer and availability of tissue was delayed during the COVID-19 pandemic. METHODS: A pilot study assessing Guardant360™ cfDNA-NGS in patients with radiological-suspected advanced-stage lung cancer was performed at an academic cancer centre during COVID-19. Variants were tiered using AMP/ASCO/CAP guidelines and discussed at a tumour molecular board. The primary endpoint was the proportion of patients who commenced targeted treatment based on cfDNA-NGS results without tissue molecular results, predicted to be ≥ 10%. RESULTS: Between April 2020-May 2021, 51 patients were enrolled; 49 were evaluable. The median age was 71 years, 43% were never-smokers, 86% had stage IV disease. 80% of evaluable cfDNA-NGS were informative (tumour-derived cfDNA detected). cfDNA-NGS detected 30 (61%) AMP/ASCO/CAP tier 1 variants, including 20 additional tier 1 variants compared to tissue testing. Three patients with non-informative cfDNA-NGS had tier 1 variants identified on tissue testing. Eleven (22%; 95%CI 12%-27%) patients commenced targeted therapy based on cfDNA-NGS results without tissue molecular results, meeting the primary endpoint. Median time to results was shorter for cfDNA-NGS compared to standard-of-care tissue tests (9 versus 25 days, P < 0.0001). CONCLUSION: Blood-first cfDNA-NGS in NSCLC patients increased the breadth and rapidity of detection of actionable variants with high tissue concordance and led to timely treatment decisions. A blood-first approach should be considered to improve the speed and accuracy of therapeutic decision-making.

A study on the demographic, clinical, and radiological profile of lineage B.1.1.7 (United Kingdom) strain Covid-19 patients at Telangana institute of medical sciences and research, Hyderabad

Background: Emergence of variants with specific mutations in key epitopes in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) raises concerns pertinent to its severity. Aims and Objectives: To assess the demographics, clinico-radiological pattern, and outcome of reverse transcription-polymerase chain reaction (RT-PCR) positive isolated coronavirus disease 2019 (COVID-19) patients arrived from the United Kingdom (UK). Materials and Methods: A cross-sectional, observational study was conducted in RT-PCR positive COVID-19 patients arrived from the UK, from December 2020 to February 2021. Nasopharyngeal samples of all patients were sent for whole-genome sequencing of SARS-CoV-2. The aimed parameters were compared between the B.1.17 positive and non-B.1.1.7 groups, among the people, arrived from the UK. All statistical tests with P<0.05 were considered significant. Results: A total of 59 SARS-CoV2 infected patients, who arrived from the UK, were isolated from December 2020 to February 2021 at Telangana Institute of Medical Sciences hospital, Hyderabad, were enrolled in the study. Of these, 27 patients (mean age-31.81±11.28 years) were infected with the B.1.1.7, diagnosed by whole genomic sequencing. Males were predominant in our study. Personal habits such as smoking, alcohol intake were higher among the sequenced group with a significant P<0.05. The most common symptoms observed in the sequenced group were cough (22.22%), sore throat (22.22%), cold (11.11%), fever (11.11%), and in the unsequenced group were cough (22.22%), cold (6.25%), fever (6.25%). In the sequenced group, chest X-ray posteroanterior view was normal in 74%, patchy ground glass opacities was observed in 25.92% patients, whereas in the unsequenced group it was 84.37% and 15.62%, respectively. Asymptomatic patients, observed in the sequenced and unsequenced group were 48.18% and 78.12%, respectively, and symptomatic patients were 51.85% and 21.87%, respectively. We found a statistically significant difference between sequenced and un sequenced patients in the asymptomatic group with a significant P<0.05. In the sequenced and unsequenced group, mild cases were 48.18% and 18.75%, moderate cases were 3.7% and 3.12%, respectively. We found no evidence of an association between disease severity and lineage B.1.17. Conclusion: Our data, within the context and limitations of a real-world study, provide initial reassurance that severity in hospitalized patients with B.1.1.7 is not markedly different from severity in those without B.1.1.7. [ FROM AUTHOR] Copyright of Asian Journal of Medical Sciences is the property of Manipal Colleges of Medical Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka.

Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021. Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages. Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country. Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage.

Genomic investigation of a household SARS-CoV-2 disease cluster in Arizona involving a cat, dog, and pet owner.

Arizona's COVID-19 and Pets Program is a prospective surveillance study being conducted to characterize how SARS-CoV-2 impacts companion animals living in households with SARS-CoV-2-positive individuals. Among the enrolled pets, we identified a SARS-CoV-2-infected cat and dog from the same household; both animals were asymptomatic but had close contact with the symptomatic and SARS-CoV-2-positive owner. Whole genome sequencing of animal and owner specimens revealed identical viral genomes of the B.1.575 lineage, suggesting zoonotic transmission of SARS-CoV-2 from human to at least one pet. This is the first report of the B.1.575 lineage in companion animals. Genetically linking SARS-CoV-2 between people and animals, and tracking changes in SARS-CoV-2 genomes is essential to detect any cross-species SARS-CoV-2 transmission that may lead to more transmissible or severe variants that can affect humans. Surveillance studies, including genomic analyses of owner and pet specimens, are needed to further our understanding of how SARS-CoV-2 impacts companion animals.