key: cord-0918083-u4v13f7v
authors: Rose, R.; Nolan, D. J.; LaFleur, T. M.; Lamers, S. L.
title: Outbreak of P.3 (Theta) SARS-CoV-2 emerging variant of concern among food service workers in Louisiana
date: 2021-07-29
journal: nan
DOI: 10.1101/2021.07.28.21259040
sha: 8181a0bd89c5453f57098c0838c69bb6575c2b90
doc_id: 918083
cord_uid: u4v13f7v

In May, 2021, during routine oil and gas industrial quarantine/premobilization procedures, four individuals who recently arrived to Louisiana from the Philippines tested positive for SARS-CoV-2. Subsequent genomic analysis showed that all were infected with a Variant of Interest (P.3-Theta). This increases the number of known P.3 infections in the United States to eleven and highlights the importance of genomic surveillance within industries that are prone to rapidly spread the infection.

Many industries have implemented extensive safety measures to reduce workplace transmission risk during the COVID-19 pandemic. These policies have been imperative in the offshore oil and gas industry because rig workers travel from many states and internationally. The western and central Gulf of Mexico is one of the major offshore petroleum-producing areas, incorporating >1800 rigs and thousands of employees. To prevent COVID-19 outbreaks on offshore platforms, the industry has implemented, to varying degrees, strict pre-mobilization testing and quarantine policies.

Here, we report the detection of a rare Pango lineage [1] , which infected four individuals who tested SARS-CoV-2 positive in May 2021 while quarantined in Louisiana, prior to deployment to an oil platform. These individuals were employed by a contractor to the oil and gas company, and all had recently traveled from the Philippines. Reconstruction of their timeline showed they tested negative in the Philippines, immediately prior to boarding a USA flight. Upon arrival in the USA, the workers went into a 14-day quarantine. They were retested after 9 days, at which point they were all qPCR+ and serology negative. None reported COVID-19 symptoms. The expected time interval between exposure and test positivity (3-4 days post-exposure for qPCR, >1 week postexposure for serology), as well as the workers' testing timeline (Figure 1a) , suggest a recent exposure after their flight to the United States.

To further understand the nature of the outbreak, the samples were sent to an independent laboratory (BioInfoExperts, LLC, Thibodaux, LA) for viral load and genomic evaluation ( Table 1) . Viral loads were quantified using ddPCR (BioRad). Sequencing was performed using the ARTIC protocol [2] on the Illumina MiSeq platform, followed by Pango lineage assignment [1] and mutation analysis using the FoxSeq software platform (https://bioinfox.com/foxseq/). All four . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 29, 2021. which have been linked to increased transmissibility and immune escape [7, 8] . In addition, >95%

. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 29, 2021. ; https://doi.org/10.1101/2021.07.28.21259040 doi: medRxiv preprint of P.3. sequences exhibit spike protein mutations at D614G, H1101Y, E1092K, and V1176F. Two synonymous spike protein mutations also occur at positions 593G and 875S. The four new Louisiana sequences have a unique spike mutation at Q1180H, which was not observed in any of the other P.3 sequences. A three amino acid deletion (LGV141_143del) in the spike protein reported as common in this lineage [6] was not found in the four Louisiana P.3 sequences.

The identification of a novel Louisiana P.3 cluster is of particular concern given the suite of spike mutations, the relatively low vaccination rate in Louisiana (<40%; [9] ), and the close working conditions on the oil rigs. Our results show that industrial monitoring for COVID-19 remains crucial. Fortunately, due the testing policies implemented, this particular variant was identified prior to deployment so that the workers continued quarantine until they were no longer considered a risk. Other employees have not contracted P.3 and are thought not to have been exposed. The study confirms that SARS-CoV-2 surveillance, especially in populations prone to viral spread, will remain important as the pandemic continues. 

A third party review from the WIRB-Copernicus Group (WCG IRB) concluded that this research was exempt from IRB review because it does not meet the definition of human subjects as defined in 45 CFR 46.102 . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 29, 2021. ; . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted July 29, 2021. . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted July 29, 2021. ; https://doi.org/10.1101/2021.07.28.21259040 doi: medRxiv preprint

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