SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021

Marques, Andrew; Sherrill-Mix, Scott; Everett, J.K.; Reddy, Shantan; Hokama, Pascha; Roche, Aoife M.; Hwang, Young Sun; Glascock, Abigail; Whiteside, Samantha A.; Graham-Wooten, Jevon; Khatib, Layla A.; Fitzgerald, Ayannah S.; Moustafa, Ahmed; Bianco, Colleen; Rajagopal, Swetha; Helton, Jenna; Deming, Regan; Denu, Lidiya; Ahmed, Anwar; Kitt, Eimear; Coffin, Susan; Newbern, Claire; Mell, Josh Chang; Planet, Paul J.; Badjatia, Nitika; Richards, Bonnie; Wang, Zixuan; Cannuscio, Carolyn C.; Strelau, Katherine M.; Jaskowiak‐Barr, Anne; Cressman, Leigh; Loughrey, Sean; Ganguly, Arupa; Feldman, Michael D.; Collman, Ronald G.; Rodino, Kyle G.; Kelly, Brendan J; Bushman, Frederic D.

doi:10.1128/mbio.03788-21

Cited by 14 publications

(19 citation statements)

References 55 publications

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“…To date, published reports on the SARS-CoV-2 delta variant lineage AY.3 have described infection of humans and one domestic dog [14][15][16]18]. Here, we report delta variant lineage AY.3 in fecal samples from a domestic cat who was exposed to a human with SARS-CoV-2.…”

Section: Discussionmentioning

confidence: 69%

“…Local human-derived viral sequences were gathered as described in a previous publication where sequence data can be accessed [18]. The University of Pennsylvania Institutional Review Board (IRB) reviewed the human research protocol and deemed the limited data elements extracted with positive human SARS-CoV-2 specimens to be exempt from human subject research per 45 CFR 46.104, category 4 (IRB #848605).…”

Section: Methodsmentioning

confidence: 99%

“…The fecal sample was tested for SARS-CoV We performed SARS-CoV-2 whole genome sequencing (WGS) on the two samples from the cat. We received 99.7% and 98.3% coverage with a mean coverage of 1,843 and 374 reads for the two samples respectively [18]. WGS performed by NVSL yielded nearly identical results using slightly different techniques.…”

Section: Molecular Detection and Sequencingmentioning

confidence: 99%

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Detection and Interspecies Comparison of SARS-CoV-2 Delta Variant (AY.3) in Feces from a Domestic Cat and Human Samples

Lenz

Marques

Kelly

et al. 2022

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have spilled over from humans to companion and wild animals since the inception of the global COVID-19 pandemic. However, whole genome sequencing data of the viral genomes that infect non-human animal species has been scant. Here, we detected and sequenced a SARS-CoV-2 delta variant (AY.3) in fecal samples from an 11-year-old domestic house cat previously exposed to an owner who tested positive for SARS-CoV-2. Molecular testing of two fecal samples collected 7 days apart yielded relatively high levels of viral RNA. Sequencing of the feline-derived viral genomes showed the two to be identical, and differing by between 4 and 14 single nucleotide polymorphisms in pairwise comparisons to human-derived lineage AY.3 sequences collected in the same geographic area and time period. However, several mutations unique to the feline samples reveal their divergence from this cohort on phylogenetic analysis. These results demonstrate continued spillover infections of emerging SARS-CoV-2 variants that threaten human and animal health, as well as highlight the importance of collecting fecal samples when testing for SARS-CoV-2 in animals. To the authors’ knowledge, this is the first published case of a SARS-CoV-2 delta variant in a domestic cat in the United States.

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Section: Discussionmentioning

confidence: 69%

Section: Methodsmentioning

confidence: 99%

Section: Molecular Detection and Sequencingmentioning

confidence: 99%

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Detection and Interspecies Comparison of SARS-CoV-2 Delta Variant (AY.3) in Feces from a Domestic Cat and Human Samples

Lenz

Marques

Kelly

et al. 2022

Preprint

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“…All deer genome sequences available from GISAID (n=108) were downloaded (Table S4 and S5), corresponding to samples acquired from 9/28/2020 to 2/25/2021 in Iowa and Ohio and dominated by early pandemic lineages including B.1.2 and B.1.311 9,10 . Local human isolates were derived from our SARS-CoV-2 sequencing program monitoring the Delaware Valley, including Philadelphia, PA 17,18 . This revealed several substitutions that were highly enriched or invariant in deer isolates, but rare or absent in human isolates.…”

Section: Main Textmentioning

confidence: 99%

“…To identify any deer-specific sequence polymorphisms, the alpha and delta SARS-CoV-2 sequences from deer determined here were compared to viral genomes from humans and deer reported previously. All deer genome sequences available from GISAID (n=108) were downloaded (Table S4 and S5 Local human isolates were derived from our SARS-CoV-2 sequencing program monitoring the Delaware Valley, including Philadelphia, PA 17,18 . This revealed several substitutions that were highly enriched or invariant in deer isolates, but rare or absent in human isolates.…”

Section: Main Textmentioning

confidence: 99%

Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania

Marques

Sherrill-Mix

Everett

et al. 2022

Preprint

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The SARS-CoV-2 pandemic likely began by spillover from bats to humans; today multiple animal species are known to be susceptible to infection. White-tailed deer, Odocoileus virginianus are infected in the United States at substantial levels, raising concerns about the formation of a new animal reservoir and potential of spill-back of new variants into humans1. Here we characterize SARS CoV-2 in deer from Pennsylvania (PA) sampled during fall and winter 2021. Of 93 nasal swab samples analyzed by RT-qPCR, 18 (19.3%) were positive for SARS-CoV-2. Seven whole-genome sequences were obtained, which were annotated as alpha and delta variants, the first reported observations of these lineages in deer, documenting multiple new jumps from humans to deer. The alpha lineage persisted in deer after its displacement by delta in humans, and deer-derived alpha variants diverged significantly from those in humans, consistent with a distinctive evolutionary trajectory in deer.

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Debulking different Corona (SARS-CoV-2 delta, omicron, OC43) and Influenza (H1N1, H3N2) virus strains by plant viral trap proteins in chewing gums to decrease infection and transmission

et al. 2022

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SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021

Abstract: SARS-CoV-2 vaccination is highly effective at reducing viral infection, hospitalization and death. However, vaccine breakthrough infections have been widely observed, raising the question of whether particular viral variants or viral mutations are associated with breakthrough.

Cited by 14 publications

References 55 publications

Detection and Interspecies Comparison of SARS-CoV-2 Delta Variant (AY.3) in Feces from a Domestic Cat and Human Samples

Detection and Interspecies Comparison of SARS-CoV-2 Delta Variant (AY.3) in Feces from a Domestic Cat and Human Samples

Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania

Debulking different Corona (SARS-CoV-2 delta, omicron, OC43) and Influenza (H1N1, H3N2) virus strains by plant viral trap proteins in chewing gums to decrease infection and transmission

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