Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar

Hasan, Mohammad Rubayet; Kalikiri, Mahesh Kumar Reddy; Mirza, Faheem; Sundararaju, Sathyavathi; Sharma, Anju; Xaba, Thabisile; Lorenz, Stephan; Chemaitelly, Hiam; El-Kahlout, Reham A.; Tsui, Clement K. M.; Yassine, Hadi M.; Coyle, Peter; Khal, Abdullatif Al; Bertollini, Roberto; Thani, Mohamed H. Al; Abu-Raddad, Laith J; Tang, Patrick

doi:10.1016/j.ijid.2021.09.006

Cited by 61 publications

(64 citation statements)

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“…Figure 1 shows the process for identifying eligible primary infections, reinfections, BNT162b2 breakthrough infections, and mRNA-1273 breakthrough infections. Figure 2 schematizes the six pairwise comparisons conducted between these cohorts of infections, after exact matching to the first match in a 1:1 ratio by sex, 10-year age group, reason for RT-qPCR testing, and calendar week of the RT-qPCR test, to control for differences in biology by sex and age, as well as risk of exposure to SARS-CoV-2 in Qatar 34 – 38 and variant exposure 4 – 6 , 8 , 9 , 26 – 28 (“Methods”). Only the first RT-qPCR-positive test for each individual for each infection category was used for analysis.…”

Section: Resultsmentioning

confidence: 99%

“…During this vaccination drive, Qatar experienced two back-to-back epidemic waves dominated by the Alpha 25 (B.1.1.7) and Beta 25 (B.1.351) variants, with the Beta wave contributing to most of the diagnosed infections during 2021 (Supplementary Fig. 1 ) 4 – 6 , 8 , 9 , 26 – 28 . While incidence since July 2021 has been dominated by the Delta 25 (B.1.617.2) variant 4 – 6 , 8 , 9 , 26 – 28 , the number of Delta infections remained relatively low with no epidemic wave materializing as of the end date of this study, July 11, 2021.…”

Section: Introductionmentioning

confidence: 99%

“…1 ) 4 – 6 , 8 , 9 , 26 – 28 . While incidence since July 2021 has been dominated by the Delta 25 (B.1.617.2) variant 4 – 6 , 8 , 9 , 26 – 28 , the number of Delta infections remained relatively low with no epidemic wave materializing as of the end date of this study, July 11, 2021.…”

Section: Introductionmentioning

confidence: 99%

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Relative infectiousness of SARS-CoV-2 vaccine breakthrough infections, reinfections, and primary infections

et al. 2022

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SARS-CoV-2 breakthrough infections in vaccinated individuals and in those who had a prior infection have been observed globally, but the transmission potential of these infections is unknown. The RT-qPCR cycle threshold (Ct) value is inversely correlated with viral load and culturable virus. Here, we investigate differences in RT-qPCR Ct values across Qatar’s national cohorts of primary infections, reinfections, BNT162b2 (Pfizer-BioNTech) breakthrough infections, and mRNA-1273 (Moderna) breakthrough infections. Our matched-cohort analyses of the randomly diagnosed infections show higher mean Ct value in all cohorts of breakthrough infections compared to the cohort of primary infections in unvaccinated individuals. The Ct value is 1.3 (95% CI: 0.9–1.8) cycles higher for BNT162b2 breakthrough infections, 3.2 (95% CI: 1.9–4.5) cycles higher for mRNA-1273 breakthrough infections, and 4.0 (95% CI: 3.5–4.5) cycles higher for reinfections in unvaccinated individuals. Since Ct value correlates inversely with SARS-CoV-2 infectiousness, these differences imply that vaccine breakthrough infections and reinfections are less infectious than primary infections in unvaccinated individuals. Public health benefits of vaccination may have been underestimated, as COVID-19 vaccines not only protect against acquisition of infection, but also appear to protect against transmission of infection.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Relative infectiousness of SARS-CoV-2 vaccine breakthrough infections, reinfections, and primary infections

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“…This finding also supports, in the context of the higher severity of this variant [32,50,51], the global risk associated with variants of concern, which can ignite new epidemic waves once introduced into a naïve population, even with public health restrictions and relatively high levels of natural immunity, as in the case of Qatar [13,14]. Notably, despite the initial rapid spread of the B.1.1.7 variant, this variant was replaced as the dominant variant AU : Ichangedthisvariantwasreplacedtothisvariantwas in subsequent weeks by the B.1.351 (or Beta [23]) variant shortly after it was introduced in mid-February 2021 [7,8,[26][27][28].…”

Section: Discussionmentioning

confidence: 99%

“…A surveillance system was set up to track the entry and expansion of variants of concern in Qatar and to confirm variant community transmission via real-time quantitative reverse transcription PCR (RT-qPCR) genotyping and viral genome sequencing [11,[26][27][28]. A component of the RT-qPCR surveillance included identifying B.1.1.7 using the TaqPath COVID-19 Combo Kit platform (Thermo Fisher Scientific [29]).…”

Section: Laboratory Methods and Viral Genome Sequencing And Analysismentioning

confidence: 99%

Introduction and expansion of the SARS-CoV-2 B.1.1.7 variant and reinfections in Qatar: A nationally representative cohort study

et al. 2021

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Background The epidemiology of the SARS-CoV-2 B.1.1.7 (or Alpha) variant is insufficiently understood. This study’s objective was to describe the introduction and expansion of this variant in Qatar and to estimate the efficacy of natural infection against reinfection with this variant. Methods and findings Reinfections with the B.1.1.7 variant and variants of unknown status were investigated in a national cohort of 159,003 individuals with prior PCR-confirmed infections and a national cohort of 43,127 antibody-positive individuals. Infections with B.1.1.7 and variants of unknown status were also investigated in a national comparator cohort of 150,106 antibody-negative individuals. B.1.1.7 was first identified in Qatar on 25 December 2020. Sudden, large B.1.1.7 epidemic expansion was observed starting on 18 January 2021, triggering the onset of epidemic’s second wave, 7 months after the first wave. B.1.1.7 was about 60% more infectious than the original (wild-type) circulating variants. Among persons with a prior PCR-confirmed infection, the efficacy of natural infection against reinfection was estimated to be 97.5% (95% CI: 95.7% to 98.6%) for B.1.1.7 and 92.2% (95% CI: 90.6% to 93.5%) for variants of unknown status. Among antibody-positive persons, the efficacy of natural infection against reinfection was estimated to be 97.0% (95% CI: 92.5% to 98.7%) for B.1.1.7 and 94.2% (95% CI: 91.8% to 96.0%) for variants of unknown status. A main limitation of this study is assessment of reinfections based on documented PCR-confirmed reinfections, but other reinfections could have occurred and gone undocumented. Conclusions In this study, we observed that introduction of B.1.1.7 into a naïve population can create a major epidemic wave, but natural immunity in those previously infected was strongly associated with limited incidence of reinfection by B.1.1.7 or other variants.

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Association of Prior SARS-CoV-2 Infection With Risk of Breakthrough Infection Following mRNA Vaccination in Qatar

Abu‐Raddad

Chemaitelly

Ayoub

et al. 2021

JAMA

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IMPORTANCEThe effect of prior SARS-CoV-2 infection on vaccine protection remains poorly understood.OBJECTIVE To assess protection from SARS-CoV-2 breakthrough infection after mRNA vaccination among persons with vs without prior SARS-CoV-2 infection.DESIGN, SETTING, AND PARTICIPANTS Matched-cohort studies in Qatar for the BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines. A total of 1 531 736 individuals vaccinated with either vaccine between December 21, 2020, and September 19, 2021, were followed up beginning 14 days after receiving the second dose until September 19, 2021.EXPOSURES Prior SARS-CoV-2 infection and COVID-19 vaccination. MAIN OUTCOMES AND MEASURESIncident SARS-CoV-2 infection, defined as a polymerase chain reaction (PCR)-positive nasopharyngeal swab regardless of reason for PCR testing or presence of symptoms. Cumulative incidence was calculated using the Kaplan-Meier estimator method. RESULTSThe BNT162b2-vaccinated cohort comprised 99 226 individuals with and 290 432 matched individuals without prior PCR-confirmed infection (median age, 37 years; 68% male). The mRNA-1273-vaccinated cohort comprised 58 096 individuals with and 169 514 matched individuals without prior PCR-confirmed infection (median age, 36 years; 73% male). Among BNT162b2-vaccinated persons, 159 reinfections occurred in those with and 2509 in those without prior infection 14 days or more after dose 2. Among mRNA-1273-vaccinated persons, 43 reinfections occurred in those with and 368 infections in those without prior infection. Cumulative infection incidence among BNT162b2-vaccinated individuals was an estimated 0.15% (95% CI, 0.12%-0.18%) in those with and 0.83% (95% CI, 0.79%-0.87%) in those without prior infection at 120 days of follow-up (adjusted hazard ratio for breakthrough infection with prior infection, 0.18 [95% CI, 0.15-0.21]; P < .001). Cumulative infection incidence among mRNA-1273-vaccinated individuals was an estimated 0.11% (95% CI, 0.08%-0.15%) in those with and 0.35% (95% CI, 0.32%-0.40%) in those without prior infection at 120 days of follow-up (adjusted hazard ratio, 0.35 [95% CI, 0.25-0.48]; P < .001). Vaccinated individuals with prior infection 6 months or more before dose 1 had statistically significantly lower risk for breakthrough infection than those infected less than 6 months before dose 1 (adjusted hazard ratio, 0.62 [95% CI, 0.42-0.92]; P = .02 for BNT162b2 and 0.40 [95% CI, 0.18-0.91]; P = .03 for mRNA-1273 vaccination). CONCLUSIONS AND RELEVANCEPrior SARS-CoV-2 infection was associated with a statistically significantly lower risk for breakthrough infection among individuals receiving the BNT162b2 or mRNA-1273 vaccines in Qatar between December 21, 2020, and September 19, 2021. The observational study design precludes direct comparisons of infection risk between the 2 vaccines.

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Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar

Cited by 61 publications

References 3 publications

Relative infectiousness of SARS-CoV-2 vaccine breakthrough infections, reinfections, and primary infections

Relative infectiousness of SARS-CoV-2 vaccine breakthrough infections, reinfections, and primary infections

Introduction and expansion of the SARS-CoV-2 B.1.1.7 variant and reinfections in Qatar: A nationally representative cohort study

Association of Prior SARS-CoV-2 Infection With Risk of Breakthrough Infection Following mRNA Vaccination in Qatar

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