Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing

Gregory, Devon A.; Trujillo, Mónica; Rushford, Clayton; Flury, Anna; Kannoly, Sherin; San, Kaung Myat; Lyfoung, Dustin T; Wiseman, Roger W.; Bromert, Karen; Zhou, Mingyi; Kesler, Ellen; Bivens, Nathan J.; Hoskins, Jay; Lin, Chung‐Ho; O’Connor, David H.; Wieberg, Chris G.; Wenzel, Jeff; Kantor, Rose; Dennehy, John J.; Johnson, Marc C.

doi:10.1371/journal.ppat.1010636

Cited by 50 publications

(55 citation statements)

References 57 publications

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“…1a). Several of the mutated amino acid positions present in the XBB.1(.5) and BQ.1.1 variant S glycoproteins were previously detected in cryptic lineages through wastewater sequencing 16 and virtually all of them map to key NTD and RBD antigenic sites. SARS-CoV-2 S recognizes angiotensin-converting enzyme 2 (ACE2) as its main entry receptor, leading to membrane fusion and viral entry [17][18][19][20] .…”

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confidence: 99%

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Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants

Addetia

Piccoli

Case³

et al. 2023

Preprint

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Currently circulating SARS-CoV-2 variants acquired convergent mutations at receptor-binding domain (RBD) hot spots. Their impact on viral infection, transmission, and efficacy of vaccines and therapeutics remains poorly understood. Here, we demonstrate that recently emerged BQ.1.1. and XBB.1 variants bind ACE2 with high affinity and promote membrane fusion more efficiently than earlier Omicron variants. Structures of the BQ.1.1 and XBB.1 RBDs bound to human ACE2 and S309 Fab (sotrovimab parent) explain the altered ACE2 recognition and preserved antibody binding through conformational selection. We show that sotrovimab binds avidly to all Omicron variants, promotes Fc-dependent effector functions and protects mice challenged with BQ.1.1, the variant displaying the greatest loss of neutralization. Moreover, in several donors vaccine-elicited plasma antibodies cross-react with and trigger effector functions against Omicron variants despite reduced neutralizing activity. Cross-reactive RBD-directed human memory B cells remained dominant even after two exposures to Omicron spikes, underscoring persistent immune imprinting. Our findings suggest that this previously overlooked class of cross-reactive antibodies, exemplified by S309, may contribute to protection against disease caused by emerging variants through elicitation of effector functions.

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confidence: 99%

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confidence: 99%

Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants

Addetia

Piccoli

Case³

et al. 2023

Preprint

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“…(7) Wastewater testing is a good predictor of impending community prevalence, with detection of new variants a few days to a week in advance of community prevalence ( 56 ), but sequencing wastewater samples to monitor the spread of genotypes is problematic/difficult due to sample quality and the presence of many different strains in the same sample, often at low-titer ( 57 ). Thus, a highly sensitive PCR panel that can detect variant markers would be ideal for wastewater monitoring ( 58 ). Similarly, the variant panel may also be a useful, cheaper alternative to sequencing and in vitro diagnostic (IVD) PCR assays for other types of environmental/non-clinical testing ( 59 ) (e.g., contamination/decontamination verification) ( 60 ), as RUO assays are typically less expensive than IVD assays.…”

Section: Discussionmentioning

confidence: 99%

Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform

Stanhope¹,

Peterson

Knight

et al. 2022

Front. Public Health

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Many SARS-CoV-2 variants have emerged during the course of the COVID-19 pandemic. These variants have acquired mutations conferring phenotypes such as increased transmissibility or virulence, or causing diagnostic, therapeutic, or immune escape. Detection of Alpha and the majority of Omicron sublineages by PCR relied on the so-called S gene target failure due to the deletion of six nucleotides coding for amino acids 69–70 in the spike (S) protein. Detection of hallmark mutations in other variants present in samples relied on whole genome sequencing. However, whole genome sequencing as a diagnostic tool is still in its infancy due to geographic inequities in sequencing capabilities, higher cost compared to other molecular assays, longer turnaround time from sample to result, and technical challenges associated with producing complete genome sequences from samples that have low viral load and/or high background. Hence, there is a need for rapid genotyping assays. In order to rapidly generate information on the presence of a variant in a given sample, we have created a panel of four triplex RT-qPCR assays targeting 12 mutations to detect and differentiate all five variants of concern: Alpha, Beta, Gamma, Delta, and Omicron. We also developed an expanded pentaplex assay that can reliably distinguish among the major sublineages (BA.1–BA.5) of Omicron. In silico, analytical and clinical testing of the variant panel indicate that the assays exhibit high sensitivity and specificity. This panel can help fulfill the need for rapid identification of variants in samples, leading to quick decision making with respect to public health measures, as well as treatment options for individuals. Compared to sequencing, these genotyping PCR assays allow much faster turn-around time from sample to results—just a couple hours instead of days or weeks.

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“…For samples processed at the University of Missouri, samples were processed as previously described 17 . Briefly, wastewater samples were centrifuged at 3000×g for 10 min and filtered through a 0.22 μM polyethersulfone membrane (Millipore, Burlington, MA, USA).…”

Section: Supplemental Online Methodsmentioning

confidence: 99%

Human origin ascertained for SARS-CoV-2 Omicron-like spike sequences detected in wastewater: a targeted surveillance study of a cryptic lineage in an urban sewershed

Shafer

Gregory

Bobholz

et al. 2022

Preprint

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Importance: The origin of highly divergent "cryptic" SARS-CoV-2 Spike sequences, which appear in wastewater but not clinical samples, is unknown. These wastewater sequences have harbored many of the same variants that later emerged in Omicron. If these enigmatic sequences are human-derived and transmissible, they could both be a source of future variants and a valuable tool for forecasting sequences that should be incorporated into vaccines and therapeutics. Objective: To determine whether enigmatic SARS-CoV-2 lineages detected in wastewater have a human or non-human (i.e., animal) source. Design: On January 11, 2022, an unusual Spike sequence was detected in municipal wastewater from a metropolitan area. Over the next four months, more focused wastewater sampling resolved the source of this variant. Setting: This study was performed in Wisconsin, United States, which has a comprehensive program for detecting SARS-CoV-2 in wastewater. Participants: Composite wastewater samples were used for this study; therefore, no individuals participated. Main Outcome(s) and Measure(s): The primary outcome was to determine the host(s) responsible for shedding this variant in wastewater. Both human and non-human hosts were plausible candidates at the study's outset. Results: The presence of the cryptic virus was narrowed from a municipal wastewater sample (catchment area >100,000 people) to an indoor wastewater sample from a single facility (catchment area ~30 people), indicating the human origin of this virus. Extraordinarily high concentrations of viral RNA (~520,000,000 genome copies / L and ~1,600,000,000 genome copies / L in June and August 2022, respectively) were detected in the indoor wastewater sample. The virus sequence harbored a combination of fixed nucleotide substitutions previously observed only in Pango lineage B.1.234, a variant that circulated at low levels in Wisconsin from October 2020 to February 2021. Conclusions and Relevance: High levels of persistent SARS-CoV-2 shedding from the gastrointestinal tract of an infected individual likely explain the presence of evolutionarily advanced, "cryptic variants" observed in some wastewater samples.

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Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing

Cited by 50 publications

References 57 publications

Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants

Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants

Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform

Human origin ascertained for SARS-CoV-2 Omicron-like spike sequences detected in wastewater: a targeted surveillance study of a cryptic lineage in an urban sewershed

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