Ongoing debates over the propriety—and legality—of applying stay-at-home orders to houses of worship have now spilled over into federal courthouses around the country. Churches in California, Kansas, Kentucky, Mississippi, and New Mexico have filed lawsuits alleging that decisions over which institutions do and don’t get to stay open amid the COVID-19 pandemic infringe on religious liberty. By allowing essential institutions to remain open, but shuttering houses of worship, these churches allege that stay-at-home orders impermissibly target religious institutions in violation of the First Amendment. After all, they say, why should liquor stores remain open while churches must remain closed?These debates took a disturbing turn last Tuesday when New York Mayor Bill de Blasio lashed out against “the Jewish community” on Twitter, sending a “message” that he would “instruct the NYPD to proceed immediately to summons or even arrest those who gather in large groups.” Jewish groups from across the political and ideological spectrum denounced the mayor for fomenting anti-Semitism during already tense times in New York City. Amazingly, given an opportunity the very next day to apologize, de Blasio doubled down, explaining that the failure to abide by the stay-at-home orders was a uniquely Jewish problem. “It has not happened other places,” he explained, “let’s be honest.”Honesty, no doubt, is something to be valued. But if de Blasio’s goal was to prevent mass gatherings within the Jewish community—and not simply lay off blame for his handling of the coronavirus epidemic on a convenient target, his words may have the opposite of their intended effect. Indeed, sending a “message” to a religious community that government will target them for enhanced legal enforcement of stay-at-home orders represents the very kind of government response that the Supreme Court has explicitly prohibited as impermissible religious discrimination.The coronavirus crisis is a watershed moment for religious liberty. Government officials, presented with an unprecedented public health crisis, are making complex decisions in real time—and those decisions are increasingly clashing with the beliefs of faith communities who look to their institutions to provide meaning in increasingly frightening times. Since 1990, the Supreme Court has explained that the First Amendment prohibits targeting religion unless it is absolutely necessary to protect a vital government interest. But as we are learning during the COVID-19 crisis, whether it is the disparate treatment facing churches or a mayoral tweetstorm, ensuring government compliance with that principle is far from simple.Part of the problem is that the Supreme Court has never quite been clear on the outer boundaries of what counts as targeting religion. In its landmark 1990 decision, Employment Division v. Smith, the Supreme Court explained that the prohibition required all laws to be both neutral and generally applied. This second requirement—general applicability—seemed to capture the notion that laws must be applied across the board to avoid targeting religion. One way to think about the requirement is that when a law has too many secular exceptions, but fails to make similar accommodations for religion, it helps unmask underlying discrimination.Consider the following case: In 1993, the Supreme Court addressed a Santeria church’s religious liberty claim, alleging that the city of Hialeah, Florida, had adopted rules, ostensibly to prohibit animal cruelty and promote public health, that were in reality a ban targeted at its animal sacrifice ritual. The court found in favor of the church, concluding that the law failed both religious-liberty requirements; it was neither neutral nor generally applicable. When it came to the second category, the court noted that the purported purpose of the ordinance prohibiting animal sacrifice was to prevent, in part, animal cruelty. And yet the law still permitted the killing of animals for a variety of reasons, including fishing, hunting wild hogs, euthanasia for stray animals, and in the interest of medical science. The host of exceptions pointed to a different explanation as to the underlying object of the ordinance; the failure to apply the law generally provided evidence of constitutionally impermissible discriminatory intent.Some courts, however, have pushed beyond this argument linking the requirement of general applicability and intentional discrimination. Maybe the most well-known example is a 1999 federal case out of Newark, New Jersey, decided by then-judge (and now Supreme Court Justice) Samuel Alito. Two Muslim police officers filed suit against the Newark Police Department for enforcing a rule requiring officers to shave their beards. The purpose of the law, according to the police department, was to ensure the uniform appearance of officers. But the fact that officers could receive a medical exception from the shaving requirement, led the court to find in favor of the Muslim police officers: If the Newark Police Department was willing to have a secular exception that undermined its objective in uniform appearance, then it also needed to allow a religious exception as well. To do otherwise would devalue religious reasons as measured against secular reasons, and it is precisely such devaluing that the requirement of general applicability is meant to prohibit.This decision, taken to its logical conclusion, opens the door to striking down laws that have secular exceptions on First Amendment grounds where the law fails to provide religious exceptions as well—and to do so even where there is no allegation of intentional discrimination. While the lack of a religious exception might not prove intentional discrimination, the privileging of secular exceptions over religious exceptions might be seen as a form of implicit bias that is also constitutionally prohibited.This debate over how to view the requirement of generally applicability—does it prohibit overt discrimination or does it prohibit implicit bias as well—runs to the heart of many of the church lawsuits against stay-at-home orders. The clear objective of stay-at-home orders is to protect public health in the midst of an unprecedented pandemic. But stay-at-home orders classify institutions into essential and nonessential categories, applying different sets of rules on the basis of that distinction. In a number of jurisdictions, these stay-at-home orders prohibit houses of worship from holding in-person worship services. If what the law cares about is intentional discrimination, states classifying houses of worship as nonessential—and thereby prohibiting them from holding worship services—are likely to overcome constitutional challenges. But if the law cares about how the doling out of limited exceptions suggests implicit bias, then stay-at-home orders may encounter judicial pushback.These COVID-19-related lawsuits serve as a useful guide for another reason: They provide a clear picture of religious liberty pitfalls that government officials must avoid. If government wants to ensure that its public health rules are enforceable, then they must avoid—at all costs—running afoul of the requirement that all laws remain neutral with respect to religion. Indeed, while the Supreme Court has provided limited guidance on the general applicability front, it has been increasingly clear about what kind of evidence it will use to determine when a law is not neutral with respect to religion.Consider again the 1993 animal sacrifice case. Not only did the court conclude that the city’s ordinance was not generally applicable, but it also was clear that the law was not neutral. To do so, it highlighted how both the text of the ordinance (which used religious terminology like “sacrifice” and “ritual”) and the application of the law (which in practice only applied to ritual sacrifice) demonstrated that the law constituted prohibited religious discrimination. As part of that analysis, the court noted that the city council’s own enactment—which “expressed concern that certain religions may propose to engage in practices which are inconsistent with public morals, peace or safety”—appeared to target religion.In 2018, the Supreme Court went even further. The Colorado Civil Rights Commission (CCRC) found a baker liable for violating the state’s anti-discrimination law by refusing to bake a cake for a same-sex couple. The baker, however, argued that forcing him to do so violated his religious liberty rights. The Supreme Court found in favor of the baker because it concluded that one of the members of the CCRC, had made statements manifesting “hostility” toward religion. For example, the commissioner compared the baker’s conduct to slavery and the Holocaust, bemoaning these sorts of “despicable pieces of rhetoric” when people “use their religion to hurt others.” Based, in part, on these statements, the court held that the adjudication of the baker’s claims was not neutral. In so doing, the court made clear that it would look not only to the text or application of a rule, but it would also look to contemporaneous statements made by government officials to discern whether a law or a law’s enforcement was motivated by an underlying hostility toward religion.A church in Mississippi has already filed a federal lawsuit alleging that they were selectively targeted by police officers who issued $500 tickets to congregants who attended drive-in Easter services. According to their complaint, the mayor was attempting to make an example of the church; or as the mayor allegedly put it in a subsequent call with faith leaders, he was trying to send a “message” to the community. Those allegations have garnered the attention of the Department of Justice, which has intervened in the case by filing a statement of interest.One would think that any official concerned with public health stakes over COVID-19 would avoid making any statements that might be construed as evidencing religious discrimination. By choosing to do the exact opposite, de Blasio exposed any future enforcement actions he might take to legal scrutiny, undermining his ability to successfully achieve his purported objective of protecting the public’s health. In light of the law’s relative clarity when it comes to the constitutional demands of religious neutrality, de Blasio’s tweets become even more irresponsible.While government must, no doubt, do whatever is in its power to protect public health, it must also think carefully about the kinds of exceptions it grants to stay-at-home orders. The way we draw lines exposes not only our collective values, but also potentially our implicit biases. If, as many have suggested, de Blasio grossly mischaracterized the conduct of the New York Jewish community, then he has besmirched a faith community and thereby exposed it to all the dangers associated with promoting anti-Semitic tropes. But what might be worse is if de Blasio’s purported truth-telling was accurate; it would mean that he disarmed New York City’s ability to enforce vital regulations against those that presented what he believed to be the greatest danger to public health. Either way, his tweets have put New Yorkers in danger.