Asymptomatic Reinfection in 2 Healthcare Workers From India With Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2

TO THE EDITOR—To et al [1] recently reported a case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection confirmed by genome sequencing. Additional reports of genetically characterized reinfections have emerged [2, 3], raising pertinent questions on the longevity of immune response in SARS-CoV-2 infection. In all previous reports, patients had symptoms in 1 or both of the episodes. Here we report asymptomatic SARS-CoV-2 reinfection in 2 healthcare workers detected during routine surveillance. The report highlights the possibility of undetected SARS-CoV-2 reinfections and the need for surveillance of SARS-CoV-2 reinfections in healthcare systems.

We describe 2 individuals, a 25-year-old man (I1) and 28-year-old woman (I2), both healthcare workers posted in the coronavirus disease 2019 (COVID-19) unit of a tertiary hospital in North India, who tested positive for SARS-CoV-2 by reverse-transcription polymerase chain reaction (RT-PCR) on 5 May 2020 and 17 May 2020, respectively. Though both individuals were asymptomatic, they were hospitalized as per institutional policy on 5 May and 18 May, respectively. Subsequently, they tested negative for SARS-CoV-2 by RT-PCR on 13 May and 27 May, respectively. After resuming duties in the hospital, the 2 individuals tested positive again for SARS-CoV-2 on 21 August and 5 September and further tested negative on the 14th and sixth days, respectively. Both individuals were again asymptomatic but had a higher viral load on the second episode of reinfection (cycle threshold values of 36 and 16.6 for I1 and 28.16 and 16.92 for I2 for the first and second episodes, respectively). The timeline of the 2 episodes of infection in the individuals are summarized in Figure 1A.

Figure 1.

A, Timelines of severe acute respiratory syndrome coronavirus 2 in individuals I1 and I2. B, Genetic variants in isolates for the 2 episodes (E1 and E2) for individuals I1 and I2. Nonsynonymous variants have been underlined and the gaps in the genome are marked in gray. Abbreviation: RT-PCR; reverse-transcription polymerase chain reaction.

Since RNA from the nasopharyngeal/oropharyngeal swabs were archived, after informed consent (IHEC-CSIR-IGIB/IHEC/2020–21/01) the sequencing-ready libraries were prepared using capture-based (TWIST Biosciences) as well as amplicon-based (COVIDSeq, Illumina) approaches. The libraries were sequenced on 75 bp × 2 paired-end recipe on Illumina MiSeq. Genomes were assembled at an average of 13 684X coverage after merging the datasets, partially covering the SARS-CoV-2 reference genome (NC_045512.2) at 89.08% and 99.96%, respectively, for the 2 episodes for I1 and 85.60% and 92.14% for I2. Analysis of the genomes using a previously published protocol [4] for loci covered in both the genomes revealed 9 and 10 unique variant differences between the virus isolates from the 2 episodes of infection for I1 and I2, respectively (Figure 1B). Of the unique variants between the pair of samples, 7 variants each for the 2 individuals mapped to predicted immune epitopes [5].

Taken together, our analysis suggests that asymptomatic reinfection may be a potentially underreported entity. Genetically distinct SARS-CoV-2 rules out persistent viral shedding or reactivation. Both individuals had a higher viral load during reinfection, highlighting the need for continuous surveillance. It is noteworthy that a genetic variant 22882T>G (S: N440K) found during reinfection in I2 possibly confers resistance to neutralizing antibodies [6]. To the best of our knowledge, this is one of the earliest reports of genetically characterized reinfection from India.

Notes

Acknowledgments. The authors thank Krishna Latha Thammineni, Ravi Kumar Chaudhary, and Abhinav Jain for assistance in data collection and Anjali Bajaj for assistance in preparing the manuscript. The authors also acknowledge Mercy Rophina, Afra Shamnath, and Mohit Mangla for the compilation of functionally relevant variants used in this analysis.

Financial support. This work was supported by the Council of Scientific and Industrial Research (CSIR) India (grants CODEST and MLP2005). A. J., B. J., M. K. D., and P. S. acknowledge a research fellowship from CSIR India. D. S. acknowledges a research fellowship from Intel.

Potential conflicts of interest. V. S. reports grants from Sanofi Genzyme and technology licensing from Dr Lal Path Labs and Genique Life Sciences, outside the submitted work. All other authors report no potential conflicts of interest.

All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

Author notes

V. G., R. C. B., and A. J. contributed equally to this work.