Revisiting SARS-CoV-2 environmental contamination by patients with COVID-19: The Omicron variant does not differ from previous strains

Glinert, Itai; Ben-Shmuel, Amir; Szwartcwort-Cohen, Moran; Beth-Din, Adi; Laskar, Orly; Barlev-Gross, Moria; Melamed, Sharon; Arbell, Noga; Levy, Haim; Horowitz, Netanel A.; Weiss, Shay

doi:10.1016/j.ijid.2022.03.001

Cited by 10 publications

(8 citation statements)

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“…In addition, the saliva of P16 on symptom Day 11 was still positive in virus culture, even though the patient had NAbs. Moreover, we obtained positive air and surface samples when the index patient had a positive IgG result and NAbs, which agrees with the findings of Lei et al 108 This contradicts the suggestion that NAbs solely could be a reliable marker for non‐infectivity 78 . In the view of infection control, we agree with Lei et al, 108 Tan et al 109 and Wölfel et al 110 that the risk for exposure can remain after the patient starts to seroconvert and possibly improve clinically.…”

Section: Discussionsupporting

confidence: 82%

“…Also, already low infectious doses have been shown to cause infection in an animal model 38,77 . A previous study did not observe significant differences in environmental contamination prevalence or Ct values between alpha and omicron B.1.1.529, which could further point toward a higher receptor binding affinity and immune escape properties of omicron variant 78 and enable the use of studies carried out with previous variants also when evaluating the environmental burden of newer variants.…”

Section: Discussionmentioning

confidence: 92%

“… 125 In addition to the hospital environment, we collected samples from homes where symptoms are generally less severe, the time from the onset of symptoms is shorter, and air conditioning is different from that of a hospital. Recent findings suggest that the environmental contamination is rather similar between the first variants and omicron, 78 suggesting that the results from the earlier variants can still be considered to provide valid information for the current situation.…”

Section: Discussionmentioning

confidence: 99%

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SARS‐CoV‐2 indoor environment contamination with epidemiological and experimental investigations

et al. 2022

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SARS‐CoV‐2 has been detected both in air and on surfaces, but questions remain about the patient‐specific and environmental factors affecting virus transmission. Additionally, more detailed information on viral sampling of the air is needed. This prospective cohort study (N = 56) presents results from 258 air and 252 surface samples from the surroundings of 23 hospitalized and eight home‐treated COVID‐19 index patients between July 2020 and March 2021 and compares the results between the measured environments and patient factors. Additionally, epidemiological and experimental investigations were performed. The proportions of qRT‐PCR‐positive air (10.7% hospital/17.6% homes) and surface samples (8.8%/12.9%) showed statistical similarity in hospital and homes. Significant SARS‐CoV‐2 air contamination was observed in a large (655.25 m3) mechanically ventilated (1.67 air changes per hour, 32.4–421 L/s/patient) patient hall even with only two patients present. All positive air samples were obtained in the absence of aerosol‐generating procedures. In four cases, positive environmental samples were detected after the patients had developed a neutralizing IgG response. SARS‐CoV‐2 RNA was detected in the following particle sizes: 0.65–4.7 μm, 7.0–12.0 μm, >10 μm, and <100 μm. Appropriate infection control against airborne and surface transmission routes is needed in both environments, even after antibody production has begun.

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Section: Discussionsupporting

confidence: 82%

Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 99%

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SARS‐CoV‐2 indoor environment contamination with epidemiological and experimental investigations

et al. 2022

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“…There was no significant difference in the NP swab Ct values between these two groups which would indicate that the viral load is not higher with one group compared to the other, although this may also be due to the small sample sizes. Glirnet et al also found no significant difference in contamination rates between the original, Alpha and Omicron strains of the SARS-CoV-2 virus in a COVID-19 patient ward setting: environmental samples from a hospital isolation ward and a quarantine hotel during February 2021 for the Alpha and original variants and in January 2022 for the Omicron variant 40 . Although we did find in our previous study that higher viral load (lower NP Ct value) was associated with a higher risk of contamination 14 , we did not demonstrate a similar finding with this Omicron study, which may have been due to the smaller number of patients studied.…”

Section: Discussionmentioning

confidence: 96%

Evaluation of real and perceived risk to health care workers caring for patients with the Omicron variant of the SARS-CoV-2 virus in surgery and obstetrics

Nair

Kozak

Alavi

et al. 2022

Preprint

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IntroductionThe Omicron variant of the SARS-CoV-2 virus is described as more contagious than previous variants. We sought to assess risk to healthcare workers (HCWs) caring for patients with COVID-19 in surgical/obstetrical settings, and the perception of risk amongst this group.MethodsFrom January to April, 2022, reverse transcription polymerase chain reaction was used to detect the presence of SARS-CoV-2 viral RNA in patient, environmental (floor, equipment, passive air) samples, and HCW’s masks (inside surface) during urgent surgery or obstetrical delivery for patients with SARS-CoV-2 infection. The primary outcome was the proportion of HCWs’ masks testing positive. Results were compared with our previous cross-sectional study involving obstetrical/surgical patients with earlier variants (2020/21). HCWs completed a risk perception electronic questionnaire.Results11 patients were included: 3 vaginal births and 8 surgeries. 5/108 samples (5%) tested positive (SARS-CoV-2 Omicron) viral RNA: 2/5 endotracheal tubes, 1/22 floor samples, 1/4 patient masks and 1 nasal probe. No samples from the HCWs masks (0/35), surgical equipment (0/10) and air samples (0/11) tested positive. No significant differences were found between the Omicron and 2020/21 patient groups’ positivity rates (Mann-Whitney U test, p = 0.838) or the level of viral load from the nasopharyngeal swabs (p = 0.405). Nurses had a higher risk perception than physicians (p = 0.038).ConclusionNo significant difference in contamination rates were found between SARS-CoV-2 Omicron BA.1 and previous variants in surgical/obstetrical settings. This is reassuring as no HCW mask was positive and no HCW tested positive for COVID-19 post-exposure.

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“…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. Although not the focus of this study, very limited preliminary studies have also been conducted using our RT-qPCR assays to test for SARS-CoV-2 variants in wastewater samples (unpublished data).…”

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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Revisiting SARS-CoV-2 environmental contamination by patients with COVID-19: The Omicron variant does not differ from previous strains

Cited by 10 publications

References 10 publications

SARS‐CoV‐2 indoor environment contamination with epidemiological and experimental investigations

SARS‐CoV‐2 indoor environment contamination with epidemiological and experimental investigations

Evaluation of real and perceived risk to health care workers caring for patients with the Omicron variant of the SARS-CoV-2 virus in surgery and obstetrics

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

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