What is the genomic diversity of SARS-CoV-2 infections within households?

In a recent study posted on medrex sib*Preprint server, researchers assessed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the home.

Background

Ribonucleic acid (RNA) viruses typically evolve and accumulate mutations as they grow in scale. This provides an evolutionary relationship between a series of cases that holds important data on the mechanisms driving epidemics forward. Similarly, data sets on SARS-CoV-2 can be used to infer transmission links between coronavirus disease 2019 (COVID-19) patients in hospitals and other similar settings.

About research

In this study, researchers used whole-genome sequencing (WGS) of the SARS-CoV-2 population to infer transmission chains within households with at least two SARS-CoV-2-infected individuals.

The Coronavirus Household Assessment and Respiratory Testing (C-HEaRT) study included households in Utah and New York from August 2020 to February 2021, and from September 2020 to August 2021. SARS-CoV-2 infection was monitored.

Additionally, the Community Organized for Arbovirus Prevention (COPA) produced the COCOVID study to assess the epidemiology of COVID-19 and enroll households from Ponce, Puerto Rico.

Eligible households in the C-HEaRT study had at least one child between the ages of 0 and 17 years, but eligible individuals had resided in the household for at least three consecutive months and completed the study study. and was willing to self-collect, reporting symptoms weekly. breath sample.

Participants were required to self-collect mid-turbinate nasal samples weekly and swab into viral transport medium, regardless of disease symptoms. The team contacted participants weekly by email or text message to ask if they had experienced symptoms of COVID-19-like (CLI) or other illnesses. Additionally, participants were asked to self-collect additional nasal swabs after the onset of CLI symptoms. In this study, CLI was defined as one or more of the following symptoms: fever, cough, sore throat, shortness of breath, diarrhea, chills, muscle aches, and changes in smell or taste. A respiratory sample was shipped and analyzed. COVID-19-positive samples from sample households detected within 14 days of each other were considered epidemiologically related.

SARS-CoV-2 genome sequencing was performed for all samples with a reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold of ≤30 in either SARS-CoV-2 nucleocapsid protein 1 or 2 targets Executed. RNA was extracted from the collected swab samples and reverse transcribed before SARS-CoV-2 complementary deoxyribonucleic acid (cDNA) amplification was performed.

result

The C-HEaRT and COCOVID studies actively monitored participants for COVID-19 infection and CLI symptoms in 706 households housing 2,369 participants. The cumulative incidence of COVID-19 during the study period was 11% in Utah, 7% in New York, and 5% in Puerto Rico.

Of the 706 households, 56 had ≤2 participants who tested positive for COVID-19 within 14 days, indicating household transmission. In addition, 26 households presented high-quality continuous data for two or more contemporaneous cases. Notably, the SARS-CoV-2 clades and lineages detected were the same among individuals living in the same household, reflecting the virus that predominated in the United States during the corresponding period.

Nearly 15 of the 26 households surveyed had indistinguishable consensus sequences grouped in the corresponding phylogenetic tree. Because these cases were epidemiologically linked, they can be considered sequence-confirmed infectious events. The team also found several tree structures with monophyletic groups with indistinguishable contemporaneous sequences, derived from non-household members from the same region. Two of his households in New York showed several such sequences when the SARS-CoV-2 B.1.526 (iota) variant was rampant in the United States. This indicates that even small sampling levels showed viral sequences that were indistinguishable from infected individuals living in the same area with presumed no epidemiological links.

Eleven households showed consensus viral sequences from one or more household members, but differed only at one to two positions. Moreover, the tree corresponding to all cases in such households had ancestor/descendant relationships and/or viral sequence linkages.

Some of the genealogies were phylogenetically distinct from contemporaneous regional sequences. These tree structures show the chain of transmission. However, the small sample size raises questions about whether connections between household members and the larger community have been lost.

Conclusion

The findings highlight that the integration of SARS-CoV-2 epidemiological and serial data can prove to be a powerful tool in research. COVID-19 infectionThe researchers believe that future studies of viral transmission in hospitals, homes, and similar collective settings can utilize Bayesian methods that integrate epidemiological and sequential information to improve inference.

*Important Notices

medRxiv publishes non-peer-reviewed, preliminary scientific reports and should not be considered conclusive, to guide clinical practice/health-related actions, or to be treated as established information .